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comparative_genomics.sh
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# phylogenetic analysis (funannotate compare)
# download data from NCBI and prepare for analysis
funannotate util gff2tbl -g <(zcat Birgus.latro.genome.gff.gz) -f <(zcat Birgus.latro.genome.fasta.gz) > Birgus.latro.tbl
funannotate util tbl2gbk -i Birgus.latro.tbl -f <(zcat Birgus.latro.genome.fasta.gz) -s "Birgus latro" --isolate Birgus
funannotate util gff2tbl -g <(zcat Panulirus.ornatus.genome.gff.gz) -f Panulirus.ornatus.genome.fasta > Panulirus.ornatus.tbl
funannotate util tbl2gbk -i Panulirus.ornatus.tbl -f Panulirus.ornatus.genome.fasta -s "Panulirus ornatus" --isolate ornatus
funannotate util gff2tbl -g <(zcat Paralithodes.camtschaticus.genome.gff.gz) -f Paralithodes.camtschaticus.genome.fasta > Paralithodes.camtschaticus.tbl
funannotate util tbl2gbk -i Paralithodes.camtschaticus.tbl -f Paralithodes.camtschaticus.genome.fasta -s "Paralithodes camtschaticus" --isolate camtschaticus
funannotate util gff2tbl -g <(zcat Additional_file_4_Bachvaroff_Csap_CDS.GFF.gz) -f Additional_file_1_Bachvaroff_Csap_genome.fasta > Callinectes.sapidus.tbl
funannotate util tbl2gbk -i Callinectes.sapidus.tbl -f Additional_file_1_Bachvaroff_Csap_genome.fasta -s "Callinectes sapidus" --isolate Callinectes
funannotate util gff2tbl -g GCF_017591435.1_ASM1759143v1_genomic.gff -f GCF_017591435.1_ASM1759143v1_genomic.fna > Portunus.trituberculatus.tbl
funannotate util tbl2gbk -i Portunus.trituberculatus.tbl -f GCF_017591435.1_ASM1759143v1_genomic.fna -s "Portunus trituberculatus" --isolate Portunus
funannotate util gff2tbl -g GCF_024679095.1_ASM2467909v1_genomic.gff -f GCF_024679095.1_ASM2467909v1_genomic.fna > Eriocheir.sinensis.tbl
funannotate util tbl2gbk -i Eriocheir.sinensis.tbl -f GCF_024679095.1_ASM2467909v1_genomic.fna -s "Eriocheir sinensis" --isolate Eriocheir
funannotate util gff2tbl -g GCA_016584305.1_ASM1658430v1_genomic.gff -f GCA_016584305.1_ASM1658430v1_genomic.fna > Chionoecetes.opilio.tbl
funannotate util tbl2gbk -i Chionoecetes.opilio.tbl -f GCA_016584305.1_ASM1658430v1_genomic.fna -s "Chionoecetes opilio" --isolate Chionoecetes
# run analysis
funannotate compare --input ../hifiasm-assembly-Eric/Cinc/HIFIASM/funannotate.AUG.Cinc_v1.10/annotate_results/Cinc_2.gbk ../hifiasm-assembly-Eric/Mani/HIFIASM/funannotate.AUG.Mani_v1.9/annotate_results/Mani_2.gbk ncbi_files/Birgus.latro/annotate_results/Birgus_latro_2.gbk ncbi_files/Callinectes_sapidus_Callinectes.gbk ncbi_files/Eriocheir_sinensis_Eriocheir.gbk ncbi_files/Panulirus_ornatus_ornatus.gbk ncbi_files/Paralithodes_camtschaticus_Paralithodes_camtschaticus_2.gbk ncbi_files/Portunus_trituberculatus_Portunus.gbk ncbi_files/Chionoecetes_opilio_Chionoecetes.gbk --out crab_comp_6 --cpus 12
#-------------------------------------------------------
#[Oct 05 10:46 AM]: OS: CentOS Linux 7, 24 cores, ~ 264 GB RAM. Python: 3.8.12
#[Oct 05 10:46 AM]: Running 1.8.11
#[Oct 05 10:46 AM]: Now parsing 9 genomes
#[Oct 05 10:46 AM]: working on Cinc
#[Oct 05 10:50 AM]: working on Mani
#[Oct 05 10:57 AM]: working on Birgus latro
#[Oct 05 11:13 AM]: working on Callinectes sapidus Callinectes
#[Oct 05 11:15 AM]: working on Eriocheir sinensis Eriocheir
#[Oct 05 11:22 AM]: working on Panulirus ornatus ornatus
#[Oct 05 11:32 AM]: working on Paralithodes camtschaticus Paralithodes_camtschaticus
#[Oct 05 11:38 AM]: working on Portunus trituberculatus Portunus
#[Oct 05 11:40 AM]: working on Chionoecetes opilio Chionoecetes
#[Oct 05 11:43 AM]: No secondary metabolite annotations found
#[Oct 05 11:43 AM]: Summarizing PFAM domain results
#[Oct 05 11:43 AM]: Summarizing InterProScan results
#[Oct 05 11:43 AM]: Loading InterPro descriptions
#[Oct 05 11:43 AM]: Summarizing MEROPS protease results
#[Oct 05 11:43 AM]: found 109/125 MEROPS familes with stdev >= 1.000000
#[Oct 05 11:43 AM]: Summarizing CAZyme results
#[Oct 05 11:43 AM]: found 50/85 CAZy familes with stdev >= 1.000000
#[Oct 05 11:43 AM]: Summarizing COG results
#[Oct 05 11:43 AM]: Summarizing secreted protein results
#[Oct 05 11:43 AM]: Summarizing fungal transcription factors
#[Oct 05 11:43 AM]: Running GO enrichment for each genome
# WARNING: skipping Birgus_latro.txt as no GO terms
# WARNING: skipping Panulirus_ornatus_ornatus.txt as no GO terms
# WARNING: skipping Paralithodes_camtschaticus_Paralithodes_camtschaticus.txt as no GO terms
# WARNING: skipping Eriocheir_sinensis_Eriocheir.txt as no GO terms
# WARNING: skipping Chionoecetes_opilio_Chionoecetes.txt as no GO terms
# WARNING: skipping Portunus_trituberculatus_Portunus.txt as no GO terms
# WARNING: skipping Callinectes_sapidus_Callinectes.txt as no GO terms
#[Oct 05 11:44 AM]: Running orthologous clustering tool, ProteinOrtho. This may take awhile...
#[Oct 06 03:25 AM]: Compiling all annotations for each genome
#[Oct 06 03:36 AM]: Inferring phylogeny using iqtree
#[Oct 06 03:36 AM]: 0 single copy BUSCO orthologs found, skipping phylogeny
#[Oct 06 03:36 AM]: Compressing results to output file: crab_comp_6.tar.gz
#[Oct 06 03:46 AM]: Funannotate compare completed successfully!
# do phylogeny based on the identified SCOs
proteinortho_grab_proteins.pl -exact 'gB16087-T1,Chr_9_Csap_17611-T1,gene-GWK47_030593-T1,fileC_1_file_1_g15612-T1,gene-LOC127006660-T1,file_1_file_1_g31601-T1,g177757-T1,gP41495-T1,gene-LOC123510894-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 1.fasta
proteinortho_grab_proteins.pl -exact 'gB114813-T1,Chr_9_Csap_12770-T1,gene-GWK47_031225-T1,fileC_1_file_1_g33520-T1,gene-LOC126990734-T1,file_1_file_1_g9357-T1,g95778-T1,gP85608-T1,gene-LOC123499246-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 2.fasta
proteinortho_grab_proteins.pl -exact 'gB21586-T1,Chr_9_Csap_02118-T1,gene-GWK47_031901-T1,fileC_1_file_1_g3579-T1,gene-LOC126999981-T1,file_1_file_1_g28048-T1,g52945-T1,gP62762-T1,gene-LOC123517080-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 3.fasta
proteinortho_grab_proteins.pl -exact 'gB8577-T1,Chr_9_Csap_23679-T1,gene-GWK47_010646-T1,fileC_1_file_1_g1166-T1,gene-LOC126984561-T1,file_1_file_1_g15865-T1,g39521-T1,gP29262-T1,gene-LOC123519512-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 4.fasta
proteinortho_grab_proteins.pl -exact 'gB85204-T1,Chr_9_Csap_19002-T1,gene-GWK47_043713-T1,fileC_1_file_1_g36120-T1,gene-LOC127003472-T1,file_1_file_1_g17066-T1,g37507-T1,gP103508-T1,gene-LOC123519451-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 5.fasta
proteinortho_grab_proteins.pl -exact 'gB12409-T1,Chr_9_Csap_20776-T1,gene-GWK47_017335-T1,fileC_1_file_1_g39751-T1,gene-LOC126997902-T1,file_1_file_1_g1334-T1,g75526-T1,gP69320-T1,gene-LOC123507774-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 6.fasta
proteinortho_grab_proteins.pl -exact 'gB47310-T1,Chr_9_Csap_19765-T1,gene-GWK47_005304-T1,fileC_1_file_1_g34050-T1,gene-LOC126995066-T1,file_1_file_1_g3340-T1,g45803-T1,gP2490-T1,gene-LOC123507421-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 7.fasta
proteinortho_grab_proteins.pl -exact 'gB19114-T1,Chr_9_Csap_03644-T1,gene-GWK47_031450-T1,fileC_1_file_1_g26778-T1,gene-LOC126996496-T1,file_1_file_1_g34493-T1,g71927-T1,gP18085-T1,gene-LOC123504717-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 8.fasta
proteinortho_grab_proteins.pl -exact 'gB69710-T1,Chr_9_Csap_01868-T1,gene-GWK47_023769-T1,fileC_1_file_1_g44491-T1,gene-LOC127000118-T1,file_1_file_1_g39354-T1,g68115-T1,gP79713-T1,gene-LOC123517014-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 9.fasta
proteinortho_grab_proteins.pl -exact 'gB110454-T1,Chr_9_Csap_21982-T1,gene-GWK47_001902-T1,fileC_1_file_1_g16784-T1,gene-LOC126996831-T1,file_1_file_1_g6136-T1,g121857-T1,gP39995-T1,gene-LOC123511869-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 10.fasta
proteinortho_grab_proteins.pl -exact 'gB81577-T1,Chr_9_Csap_13663-T1,gene-GWK47_036707-T1,fileC_1_file_1_g12904-T1,gene-LOC126995834-T1,file_1_file_1_g35715-T1,g63055-T1,gP25776-T1,gene-LOC123513092-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 11.fasta
proteinortho_grab_proteins.pl -exact 'gB22908-T1,Chr_9_Csap_06897-T1,gene-GWK47_040989-T1,fileC_1_file_1_g11152-T1,gene-LOC126985403-T1,file_1_file_1_g16844-T1,g16743-T1,gP27050-T1,gene-LOC123512541-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 12.fasta
proteinortho_grab_proteins.pl -exact 'gB101912-T1,Chr_9_Csap_17957-T1,gene-GWK47_004206-T1,fileC_1_file_1_g20550-T1,gene-LOC127003324-T1,file_1_file_1_g34736-T1,g36460-T1,gP90461-T1,gene-LOC123519606-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 13.fasta
proteinortho_grab_proteins.pl -exact 'gB90532-T1,Chr_9_Csap_20746-T1,gene-GWK47_027103-T1,fileC_1_file_1_g19721-T1,gene-LOC126998005-T4,file_1_file_1_g18761-T1,g164248-T1,gP21151-T1,gene-LOC123507804-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 14.fasta
proteinortho_grab_proteins.pl -exact 'gB76588-T1,Chr_9_Csap_22236-T1,gene-GWK47_033791-T1,fileC_1_file_1_g29047-T1,gene-LOC126990107-T1,file_1_file_1_g271-T1,g140629-T2,gP94469-T1,gene-LOC123499073-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 15.fasta
proteinortho_grab_proteins.pl -exact 'gB92650-T1,Chr_9_Csap_00377-T1,gene-GWK47_051737-T1,fileC_1_file_1_g5417-T1,gene-LOC127009735-T1,file_1_file_1_g9884-T1,g43140-T1,gP20004-T1,gene-LOC123520473-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 16.fasta
proteinortho_grab_proteins.pl -exact 'gB51156-T2,Chr_9_Csap_02480-T1,gene-GWK47_000662-T1,fileC_1_file_1_g8387-T1,gene-LOC127001335-T1,file_1_file_1_g6185-T1,g71006-T2,gP86050-T1,gene-LOC123517019-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 17.fasta
proteinortho_grab_proteins.pl -exact 'gB58272-T1,Chr_9_Csap_13045-T1,gene-GWK47_004571-T1,fileC_1_file_1_g17578-T1,gene-LOC127008874-T1,file_1_file_1_g20788-T1,g7187-T1,gP64825-T1,gene-LOC123499149-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 18.fasta
proteinortho_grab_proteins.pl -exact 'gB31124-T1,Chr_9_Csap_12292-T1,gene-GWK47_010505-T1,fileC_1_file_1_g19670-T1,gene-LOC127001726-T1,file_1_file_1_g30917-T1,g68600-T1,gP63193-T2,gene-LOC123505827-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 19.fasta
proteinortho_grab_proteins.pl -exact 'gB32867-T1,Chr_9_Csap_20353-T1,gene-GWK47_003798-T1,fileC_1_file_1_g32530-T1,gene-LOC126986173-T1,file_1_file_1_g32469-T1,g29371-T2,gP23611-T1,gene-LOC123499696-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 20.fasta
proteinortho_grab_proteins.pl -exact 'gB86206-T1,Chr_9_Csap_16025-T1,gene-GWK47_050385-T1,fileC_1_file_1_g18911-T1,gene-LOC126985452-T2,file_1_file_1_g6064-T1,g142259-T1,gP51846-T1,gene-LOC123506675-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 21.fasta
proteinortho_grab_proteins.pl -exact 'gB33192-T1,Chr_9_Csap_16620-T1,gene-GWK47_027547-T1,fileC_1_file_1_g26547-T1,gene-LOC126986711-T1,file_1_file_1_g30758-T1,g54873-T1,gP3089-T1,gene-LOC123509706-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 22.fasta
proteinortho_grab_proteins.pl -exact 'gB10102-T2,Chr_9_Csap_16424-T1,gene-GWK47_006180-T1,fileC_1_file_1_g40256-T1,gene-LOC126986626-T1,file_1_file_1_g360-T1,g37630-T3,gP57867-T1,gene-LOC123509513-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 23.fasta
proteinortho_grab_proteins.pl -exact 'gB90483-T1,Chr_9_Csap_18125-T1,gene-GWK47_048101-T1,fileC_1_file_1_g32891-T1,gene-LOC127003550-T1,file_1_file_1_g11558-T1,g7060-T1,gP33512-T1,gene-LOC123519487-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 24.fasta
proteinortho_grab_proteins.pl -exact 'gB58697-T2,Chr_9_Csap_13826-T1,gene-GWK47_033413-T1,fileC_1_file_1_g11760-T1,gene-LOC126983928-T1,file_1_file_1_g14153-T1,g13139-T3,gP31803-T1,gene-LOC123508717-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 25.fasta
proteinortho_grab_proteins.pl -exact 'gB65368-T1,Chr_9_Csap_17973-T1,gene-GWK47_004193-T1,fileC_1_file_1_g33141-T1,gene-LOC127003425-T1,file_1_file_1_g16739-T1,g100384-T1,gP52-T1,gene-LOC123519674-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 26.fasta
proteinortho_grab_proteins.pl -exact 'gB93723-T1,Chr_9_Csap_03530-T1,gene-GWK47_018418-T1,fileC_1_file_1_g24215-T1,gene-LOC126996686-T1,file_1_file_1_g16106-T1,g140085-T1,gP105071-T1,gene-LOC123504915-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 27.fasta
proteinortho_grab_proteins.pl -exact 'gB11864-T1,Chr_9_Csap_14131-T1,gene-GWK47_012086-T1,fileC_1_file_1_g14154-T1,gene-LOC127005485-T1,file_1_file_1_g13743-T1,g113912-T1,gP50792-T1,gene-LOC123502791-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 28.fasta
proteinortho_grab_proteins.pl -exact 'gB67191-T1,Chr_9_Csap_19371-T1,gene-GWK47_023452-T1,fileC_1_file_1_g22529-T1,gene-LOC126996066-T1,file_1_file_1_g8971-T1,g84633-T2,gP42080-T1,gene-LOC123510213-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 29.fasta
proteinortho_grab_proteins.pl -exact 'gB78435-T1,Chr_9_Csap_16385-T1,gene-GWK47_007910-T1,fileC_1_file_1_g781-T1,gene-LOC127007726-T1,file_1_file_1_g3415-T1,g64049-T1,gP49242-T1,gene-LOC123509350-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 30.fasta
proteinortho_grab_proteins.pl -exact 'gB28245-T1,Chr_9_Csap_23387-T1,gene-GWK47_018425-T1,fileC_1_file_1_g31015-T1,gene-LOC127010043-T1,file_1_file_1_g7259-T1,g188248-T1,gP57439-T1,gene-LOC123509236-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 31.fasta
proteinortho_grab_proteins.pl -exact 'gB119001-T1,Chr_9_Csap_08030-T1,gene-GWK47_024010-T1,fileC_1_file_1_g35252-T1,gene-LOC126995704-T1,file_1_file_1_g31384-T1,g197966-T1,gP65099-T1,gene-LOC123514610-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 32.fasta
proteinortho_grab_proteins.pl -exact 'gB25344-T1,Chr_9_Csap_23913-T1,gene-GWK47_017412-T1,fileC_1_file_1_g11625-T1,gene-LOC127004938-T1,file_1_file_1_g4656-T1,g18766-T1,gP77083-T1,gene-LOC123501577-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 33.fasta
proteinortho_grab_proteins.pl -exact 'gB23557-T1,Chr_9_Csap_20695-T1,gene-GWK47_029211-T1,fileC_1_file_1_g3309-T1,gene-LOC127005058-T1,file_1_file_1_g27200-T1,g67591-T1,gP59239-T1,gene-LOC123501695-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 34.fasta
proteinortho_grab_proteins.pl -exact 'gB44777-T1,Chr_9_Csap_03212-T1,gene-GWK47_012714-T1,fileC_1_file_1_g16179-T1,gene-LOC127003770-T1,file_1_file_1_g2523-T1,g47729-T1,gP26353-T1,gene-LOC123515953-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 35.fasta
proteinortho_grab_proteins.pl -exact 'gB51005-T4,Chr_9_Csap_15619-T1,gene-GWK47_043954-T1,fileC_1_file_1_g23332-T1,gene-LOC126980297-T1,file_1_file_1_g39328-T1,g42181-T1,gP51826-T3,gene-LOC123503107-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 36.fasta
proteinortho_grab_proteins.pl -exact 'gB101563-T1,Chr_9_Csap_19803-T1,gene-GWK47_005062-T1,fileC_1_file_1_g40629-T1,gene-LOC126994590-T1,file_1_file_1_g31524-T1,g173535-T1,gP12173-T2,gene-LOC123507496-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 37.fasta
proteinortho_grab_proteins.pl -exact 'gB48628-T2,Chr_9_Csap_20720-T1,gene-GWK47_021781-T1,fileC_1_file_1_g31490-T1,gene-LOC127005222-T1,file_1_file_1_g11462-T1,g115573-T1,gP102241-T1,gene-LOC123501662-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 38.fasta
proteinortho_grab_proteins.pl -exact 'gB42810-T1,Chr_9_Csap_08829-T1,gene-GWK47_053793-T1,fileC_1_file_1_g31754-T1,gene-LOC127007526-T1,file_1_file_1_g14395-T1,g25365-T1,gP38267-T1,gene-LOC123514407-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 39.fasta
proteinortho_grab_proteins.pl -exact 'gB13841-T2,Chr_9_Csap_14327-T1,gene-GWK47_042303-T1,fileC_1_file_1_g29720-T1,gene-LOC126988228-T1,file_1_file_1_g18959-T1,g15101-T1,gP14642-T1,gene-LOC123506244-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 40.fasta
proteinortho_grab_proteins.pl -exact 'gB67148-T1,Chr_9_Csap_04436-T1,gene-GWK47_014718-T1,fileC_1_file_1_g10293-T1,gene-LOC126987532-T1,file_1_file_1_g19279-T1,g90877-T1,gP39990-T1,gene-LOC123500166-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 41.fasta
proteinortho_grab_proteins.pl -exact 'gB52717-T1,Chr_9_Csap_15629-T1,gene-GWK47_038700-T1,fileC_1_file_1_g30915-T1,gene-LOC127000438-T1,file_1_file_1_g25064-T1,g19363-T1,gP93516-T3,gene-LOC123510524-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 42.fasta
proteinortho_grab_proteins.pl -exact 'gB1715-T1,Chr_9_Csap_14490-T1,gene-GWK47_002396-T1,fileC_1_file_1_g20093-T1,gene-LOC127010143-T1,file_1_file_1_g10908-T1,g24990-T1,gP24972-T1,gene-LOC123518258-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 43.fasta
proteinortho_grab_proteins.pl -exact 'gB17094-T2,Chr_9_Csap_16711-T1,gene-GWK47_000951-T1,fileC_1_file_1_g19258-T1,gene-LOC126986874-T1,file_1_file_1_g3637-T1,g12896-T1,gP36191-T1,gene-LOC123508095-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 44.fasta
proteinortho_grab_proteins.pl -exact 'gB20858-T2,Chr_9_Csap_20546-T1,gene-GWK47_029196-T1,fileC_1_file_1_g12977-T1,gene-LOC127005255-T1,file_1_file_1_g11455-T1,g31083-T1,gP2081-T2,gene-LOC123501582-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 45.fasta
proteinortho_grab_proteins.pl -exact 'gB88543-T1,Chr_9_Csap_19186-T1,gene-GWK47_051095-T1,fileC_1_file_1_g18160-T1,gene-LOC126995979-T1,file_1_file_1_g35199-T1,g33654-T1,gP67326-T1,gene-LOC123510011-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 46.fasta
proteinortho_grab_proteins.pl -exact 'gB53509-T1,Chr_9_Csap_23630-T1,gene-GWK47_050959-T1,fileC_1_file_1_g15039-T1,gene-LOC126985373-T1,file_1_file_1_g3529-T1,g53357-T1,gP102089-T1,gene-LOC123512766-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 47.fasta
proteinortho_grab_proteins.pl -exact 'gB20848-T1,Chr_9_Csap_20544-T1,gene-GWK47_025502-T1,fileC_1_file_1_g12978-T1,gene-LOC127005239-T1,file_1_file_1_g11456-T1,g31081-T1,gP2078-T1,gene-LOC123501454-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 48.fasta
proteinortho_grab_proteins.pl -exact 'gB70720-T1,Chr_9_Csap_14600-T1,gene-GWK47_004257-T1,fileC_1_file_1_g21868-T1,gene-LOC127003267-T1,file_1_file_1_g32849-T1,g194008-T1,gP77320-T1,gene-LOC123506228-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 49.fasta
proteinortho_grab_proteins.pl -exact 'gB53610-T1,Chr_9_Csap_00940-T1,gene-GWK47_002655-T1,fileC_1_file_1_g17895-T1,gene-LOC127007650-T3,file_1_file_1_g20034-T1,g127169-T1,gP21759-T1,gene-LOC123509494-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 50.fasta
proteinortho_grab_proteins.pl -exact 'gB15546-T1,Chr_9_Csap_10672-T1,gene-GWK47_025027-T1,fileC_1_file_1_g17546-T1,gene-LOC127002170-T1,file_1_file_1_g25846-T1,g659-T1,gP43427-T1,gene-LOC123515729-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 51.fasta
proteinortho_grab_proteins.pl -exact 'gB20190-T1,Chr_9_Csap_11055-T1,gene-GWK47_040158-T1,fileC_1_file_1_g35001-T1,gene-LOC127008217-T1,file_1_file_1_g16446-T1,g147293-T1,gP8821-T2,gene-LOC123511512-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 52.fasta
proteinortho_grab_proteins.pl -exact 'gB2762-T1,Chr_9_Csap_09652-T1,gene-GWK47_031698-T1,fileC_1_file_1_g38118-T1,gene-LOC127001782-T4,file_1_file_1_g12516-T1,g137272-T1,gP98228-T1,gene-LOC123498586-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 53.fasta
proteinortho_grab_proteins.pl -exact 'gB79708-T1,Chr_9_Csap_19996-T1,gene-GWK47_007478-T1,fileC_1_file_1_g12490-T1,gene-LOC126980264-T1,file_1_file_1_g33697-T1,g27953-T1,gP10111-T1,gene-LOC123503284-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 54.fasta
proteinortho_grab_proteins.pl -exact 'gB62660-T1,Chr_9_Csap_03228-T1,gene-GWK47_019793-T1,fileC_1_file_1_g17444-T1,gene-LOC127004164-T1,file_1_file_1_g36938-T1,g81520-T1,gP40589-T1,gene-LOC123516045-T2' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 55.fasta
proteinortho_grab_proteins.pl -exact 'gB31945-T1,Chr_9_Csap_12279-T1,gene-GWK47_037993-T1,fileC_1_file_1_g14540-T1,gene-LOC127001557-T1,file_1_file_1_g12120-T1,g29496-T1,gP17139-T1,gene-LOC123505696-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 56.fasta
proteinortho_grab_proteins.pl -exact 'gB100739-T1,Chr_9_Csap_09476-T1,gene-GWK47_021462-T1,fileC_1_file_1_g27455-T1,gene-LOC127007490-T1,file_1_file_1_g37639-T1,g166631-T1,gP54985-T1,gene-LOC123503555-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 57.fasta
proteinortho_grab_proteins.pl -exact 'gB59207-T1,Chr_9_Csap_10239-T1,gene-GWK47_049999-T1,fileC_1_file_1_g16555-T1,gene-LOC127009658-T1,file_1_file_1_g32570-T1,g2763-T1,gP39568-T1,gene-LOC123515629-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 58.fasta
proteinortho_grab_proteins.pl -exact 'gB16756-T1,Chr_9_Csap_10087-T1,gene-GWK47_002586-T1,fileC_1_file_1_g34569-T1,gene-LOC126998725-T1,file_1_file_1_g19836-T1,g51447-T4,gP12911-T1,gene-LOC123498974-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 59.fasta
proteinortho_grab_proteins.pl -exact 'gB27418-T1,Chr_9_Csap_24352-T1,gene-GWK47_019484-T1,fileC_1_file_1_g36916-T1,gene-LOC126987088-T2,file_1_file_1_g27372-T1,g23937-T2,gP36051-T1,gene-LOC123505622-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 60.fasta
proteinortho_grab_proteins.pl -exact 'gB25222-T1,Chr_9_Csap_00552-T1,gene-GWK47_027824-T1,fileC_1_file_1_g16149-T1,gene-LOC126987192-T1,file_1_file_2_1651_g-T1,g44549-T1,gP14241-T1,gene-LOC123505367-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 61.fasta
proteinortho_grab_proteins.pl -exact 'gB29665-T1,Chr_9_Csap_18979-T1,gene-GWK47_046671-T1,fileC_1_file_1_g3745-T1,gene-LOC126999490-T1,file_1_file_1_g16549-T1,g51605-T3,gP2466-T1,gene-LOC123513552-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 62.fasta
proteinortho_grab_proteins.pl -exact 'gB85851-T1,Chr_9_Csap_04437-T1,gene-GWK47_014719-T1,fileC_1_file_2_24574_g-T1,gene-LOC126987531-T1,file_1_file_1_g19280-T1,g56907-T1,gP30538-T1,gene-LOC123500168-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 63.fasta
proteinortho_grab_proteins.pl -exact 'gB67402-T1,Chr_9_Csap_22127-T1,gene-GWK47_029250-T1,fileC_1_file_1_g41360-T1,gene-LOC127007644-T3,file_1_file_1_g33591-T1,g29791-T1,gP18796-T1,gene-LOC123509598-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 64.fasta
proteinortho_grab_proteins.pl -exact 'gB125984-T1,Chr_9_Csap_08677-T1,gene-GWK47_010386-T1,fileC_1_file_1_g13919-T1,gene-LOC127007501-T1,file_1_file_1_g38547-T1,g125028-T1,gP89443-T1,gene-LOC123513859-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 65.fasta
proteinortho_grab_proteins.pl -exact 'gB75435-T1,Chr_9_Csap_07452-T1,gene-GWK47_042727-T1,fileC_1_file_1_g12200-T1,gene-LOC127007023-T1,file_1_file_1_g24698-T1,g123213-T1,gP39534-T1,gene-LOC123517974-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 66.fasta
proteinortho_grab_proteins.pl -exact 'gB19614-T2,Chr_9_Csap_07600-T1,gene-GWK47_045183-T1,fileC_1_file_1_g22808-T1,gene-LOC126995408-T1,file_1_file_1_g33202-T1,g23460-T1,gP28949-T1,gene-LOC123514743-T2' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 67.fasta
proteinortho_grab_proteins.pl -exact 'gB115724-T1,Chr_9_Csap_05205-T1,gene-GWK47_035632-T1,fileC_1_file_1_g20650-T1,gene-LOC127005834-T4,file_1_file_1_g18102-T1,g64741-T1,gP24555-T1,gene-LOC123517703-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 68.fasta
proteinortho_grab_proteins.pl -exact 'gB43342-T1,Chr_9_Csap_05547-T1,gene-GWK47_013428-T1,fileC_1_file_1_g12606-T1,gene-LOC127009175-T1,file_1_file_1_g5878-T1,g27947-T2,gP102615-T1,gene-LOC123517498-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 69.fasta
proteinortho_grab_proteins.pl -exact 'gB100316-T1,Chr_9_Csap_24220-T1,gene-GWK47_039689-T1,fileC_1_file_1_g23184-T1,gene-LOC126997033-T1,file_1_file_1_g10195-T1,g32132-T1,gP41003-T1,gene-LOC123512068-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 70.fasta
proteinortho_grab_proteins.pl -exact 'gB57706-T1,Chr_9_Csap_16273-T1,gene-GWK47_005600-T1,fileC_1_file_1_g7800-T1,gene-LOC127007718-T1,file_1_file_1_g30113-T1,g24638-T1,gP34638-T1,gene-LOC123509493-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 71.fasta
proteinortho_grab_proteins.pl -exact 'gB53817-T1,Chr_9_Csap_23944-T1,gene-GWK47_042481-T1,fileC_1_file_2_5546_g-T1,gene-LOC127010128-T1,file_1_file_1_g23314-T1,g2001-T1,gP38107-T1,gene-LOC123518547-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 72.fasta
proteinortho_grab_proteins.pl -exact 'gB88925-T1,Chr_9_Csap_14229-T1,gene-GWK47_028285-T1,fileC_1_file_1_g19680-T1,gene-LOC126984019-T1,file_1_file_1_g22911-T1,g19384-T1,gP27161-T2,gene-LOC123509006-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 73.fasta
proteinortho_grab_proteins.pl -exact 'gB10877-T1,Chr_9_Csap_12215-T1,gene-GWK47_041954-T1,fileC_1_file_1_g16834-T1,gene-LOC127001619-T4,file_1_file_1_g28823-T1,g25675-T4,gP21137-T1,gene-LOC123505904-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 74.fasta
proteinortho_grab_proteins.pl -exact 'gB1590-T2,Chr_9_Csap_10967-T1,gene-GWK47_020300-T1,fileC_1_file_1_g34994-T1,gene-LOC127008396-T1,file_1_file_1_g16439-T1,g5894-T3,gP12044-T2,gene-LOC123511253-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 75.fasta
proteinortho_grab_proteins.pl -exact 'gB46585-T1,Chr_9_Csap_02291-T1,gene-GWK47_005361-T1,fileC_1_file_1_g14069-T1,gene-LOC126999717-T4,file_1_file_1_g31453-T1,g184151-T1,gP22705-T1,gene-LOC123517126-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 76.fasta
proteinortho_grab_proteins.pl -exact 'gB43299-T1,Chr_9_Csap_12148-T1,gene-GWK47_050924-T1,fileC_1_file_1_g34120-T1,gene-LOC127001665-T1,file_1_file_1_g15958-T1,g20631-T1,gP85271-T1,gene-LOC123505667-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 77.fasta
proteinortho_grab_proteins.pl -exact 'gB13840-T1,Chr_9_Csap_14326-T1,gene-GWK47_042302-T1,fileC_1_file_1_g29719-T1,gene-LOC126988227-T1,file_1_file_1_g18960-T1,g15103-T2,gP81871-T1,gene-LOC123506241-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 78.fasta
proteinortho_grab_proteins.pl -exact 'gB95967-T1,Chr_9_Csap_05499-T1,gene-GWK47_002232-T1,fileC_1_file_1_g25769-T1,gene-LOC127009377-T1,file_1_file_1_g38750-T1,g146986-T1,gP72900-T1,gene-LOC123517542-T2' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 79.fasta
proteinortho_grab_proteins.pl -exact 'gB43185-T1,Chr_9_Csap_01910-T1,gene-GWK47_004684-T1,fileC_1_file_1_g22812-T1,gene-LOC126999932-T2,file_1_file_1_g33205-T1,g19200-T1,gP20049-T1,gene-LOC123517202-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 80.fasta
proteinortho_grab_proteins.pl -exact 'gB80086-T1,Chr_9_Csap_02678-T1,gene-GWK47_037654-T1,fileC_1_file_1_g14072-T1,gene-LOC126989549-T2,file_1_file_1_g31456-T1,g7707-T1,gP45467-T1,gene-LOC123516922-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 81.fasta
proteinortho_grab_proteins.pl -exact 'gB30272-T1,Chr_9_Csap_19078-T1,gene-GWK47_004385-T1,fileC_1_file_1_g32885-T1,gene-LOC126996127-T1,file_1_file_1_g23736-T1,g42482-T1,gP28852-T1,gene-LOC123510099-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 82.fasta
proteinortho_grab_proteins.pl -exact 'gB75430-T1,Chr_9_Csap_14240-T1,gene-GWK47_006156-T2,fileC_1_file_1_g15089-T1,gene-LOC126995114-T1,file_1_file_1_g22445-T1,g85682-T1,gP78640-T1,gene-LOC123507443-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 83.fasta
proteinortho_grab_proteins.pl -exact 'gB42398-T2,Chr_9_Csap_19508-T1,gene-GWK47_037273-T1,fileC_1_file_1_g15881-T1,gene-LOC127000751-T1,file_1_file_1_g32596-T1,g19000-T2,gP17338-T1,gene-LOC123501938-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 84.fasta
proteinortho_grab_proteins.pl -exact 'gB61651-T1,Chr_9_Csap_17983-T1,gene-GWK47_044400-T1,fileC_1_file_2_34303_g-T1,gene-LOC127003448-T1,file_1_file_1_g24613-T1,g192390-T1,gP32608-T1,gene-LOC123519577-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 85.fasta
proteinortho_grab_proteins.pl -exact 'gB6707-T1,Chr_9_Csap_05310-T1,gene-GWK47_018724-T1,fileC_1_file_1_g2749-T1,gene-LOC127005954-T1,file_1_file_1_g10762-T1,g10552-T2,gP77983-T1,gene-LOC123517635-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 86.fasta
proteinortho_grab_proteins.pl -exact 'gB676-T1,Chr_9_Csap_02712-T1,gene-GWK47_047904-T1,fileC_1_file_1_g33307-T1,gene-LOC126999836-T3,file_1_file_1_g26125-T1,g99980-T1,gP16337-T1,gene-LOC123516933-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 87.fasta
proteinortho_grab_proteins.pl -exact 'gB59223-T1,Chr_9_Csap_08858-T1,gene-GWK47_036150-T1,fileC_1_file_1_g31710-T1,gene-LOC126982262-T1,file_1_file_1_g40261-T1,g23015-T1,gP90812-T1,gene-LOC123510684-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 88.fasta
proteinortho_grab_proteins.pl -exact 'gB66756-T1,Chr_9_Csap_07343-T1,gene-GWK47_017570-T1,fileC_1_file_1_g44370-T1,gene-LOC127002550-T1,file_1_file_1_g3513-T1,g249561-T1,gP64413-T1,gene-LOC123518443-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 89.fasta
proteinortho_grab_proteins.pl -exact 'gB89033-T1,Chr_9_Csap_24980-T1,gene-GWK47_043461-T1,fileC_1_file_1_g6498-T1,gene-LOC126982208-T1,file_1_file_1_g24285-T1,g100683-T1,gP82184-T1,gene-LOC123511535-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 90.fasta
proteinortho_grab_proteins.pl -exact 'gB70855-T4,Chr_9_Csap_20264-T1,gene-GWK47_002406-T1,fileC_1_file_1_g19034-T1,gene-LOC126986422-T1,file_1_file_1_g22000-T1,g37484-T1,gP15026-T1,gene-LOC123500186-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 91.fasta
proteinortho_grab_proteins.pl -exact 'gB103278-T1,Chr_9_Csap_08524-T1,gene-GWK47_043149-T1,fileC_1_file_1_g42837-T1,gene-LOC127005217-T1,file_1_file_1_g34940-T1,g64197-T1,gP95675-T1,gene-LOC123503792-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 92.fasta
proteinortho_grab_proteins.pl -exact 'gB76336-T1,Chr_9_Csap_10714-T1,gene-GWK47_005897-T1,fileC_1_file_1_g25401-T1,gene-LOC127001961-T1,file_1_file_1_g37845-T1,g59523-T1,gP74132-T1,gene-LOC123515733-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 93.fasta
proteinortho_grab_proteins.pl -exact 'gB96390-T1,Chr_9_Csap_22731-T1,gene-GWK47_024446-T1,fileC_1_file_1_g10465-T1,gene-LOC126987584-T1,file_1_file_1_g35114-T1,g177295-T1,gP87209-T1,gene-LOC123499515-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 94.fasta
proteinortho_grab_proteins.pl -exact 'gB16010-T1,Chr_9_Csap_19771-T1,gene-GWK47_045338-T1,fileC_1_file_1_g23887-T1,gene-LOC126988213-T1,file_1_file_1_g24693-T1,g44252-T2,gP32537-T1,gene-LOC123506134-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 95.fasta
proteinortho_grab_proteins.pl -exact 'gB19234-T1,Chr_9_Csap_20870-T1,gene-GWK47_049750-T1,fileC_1_file_1_g40868-T1,gene-LOC126998056-T1,file_1_file_1_g1331-T1,g118283-T1,gP46462-T1,gene-LOC123507927-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 96.fasta
proteinortho_grab_proteins.pl -exact 'gB40299-T7,Chr_9_Csap_16313-T1,gene-GWK47_049000-T1,fileC_1_file_1_g26052-T1,gene-LOC127007665-T3,file_1_file_1_g19416-T1,g18638-T5,gP69082-T1,gene-LOC123509678-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 97.fasta
proteinortho_grab_proteins.pl -exact 'gB49113-T2,Chr_9_Csap_06146-T1,gene-GWK47_044028-T1,fileC_1_file_1_g28673-T1,gene-LOC126997555-T1,file_1_file_1_g20190-T1,g65244-T1,gP102486-T1,gene-LOC123518254-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 98.fasta
proteinortho_grab_proteins.pl -exact 'gB39131-T1,Chr_9_Csap_18509-T1,gene-GWK47_020117-T1,fileC_1_file_1_g25000-T1,gene-LOC126983079-T1,file_1_file_1_g15975-T1,g33212-T2,gP24202-T1,gene-LOC123506980-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 99.fasta
proteinortho_grab_proteins.pl -exact 'gB90358-T1,Chr_9_Csap_16787-T1,gene-GWK47_035315-T1,fileC_1_file_1_g33211-T1,gene-LOC126981544-T19,file_1_file_1_g24442-T1,g9515-T1,gP90589-T1,gene-LOC123508372-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 100.fasta
proteinortho_grab_proteins.pl -exact 'gB78284-T1,Chr_9_Csap_12471-T1,gene-GWK47_001186-T1,fileC_1_file_2_37204_g-T1,gene-LOC127006975-T1,file_1_file_2_9006_g-T1,g20513-T1,gP72805-T2,gene-LOC123504475-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 101.fasta
proteinortho_grab_proteins.pl -exact 'gB95556-T1,Chr_9_Csap_15085-T1,gene-GWK47_018052-T1,fileC_1_file_1_g3043-T1,gene-LOC127008517-T1,file_1_file_1_g3732-T1,g52909-T2,gP96643-T4,gene-LOC123512188-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 102.fasta
proteinortho_grab_proteins.pl -exact 'gB131497-T1,Chr_9_Csap_03796-T1,gene-GWK47_052725-T1,fileC_1_file_1_g5860-T1,gene-LOC126996624-T2,file_1_file_1_g27673-T1,g106268-T1,gP46991-T1,gene-LOC123505227-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 103.fasta
proteinortho_grab_proteins.pl -exact 'gB51159-T3,Chr_9_Csap_21494-T1,gene-GWK47_022667-T2,fileC_1_file_1_g42783-T1,gene-LOC127001901-T1,file_1_file_1_g10349-T1,g4983-T1,gP36867-T2,gene-LOC123515355-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 104.fasta
proteinortho_grab_proteins.pl -exact 'gB60397-T1,Chr_9_Csap_02697-T1,gene-GWK47_038031-T1,fileC_1_file_1_g15023-T1,gene-LOC126981747-T1,file_1_file_1_g35807-T1,g70354-T1,gP38894-T1,gene-LOC123520208-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 105.fasta
proteinortho_grab_proteins.pl -exact 'gB20725-T2,Chr_9_Csap_07139-T1,gene-GWK47_022315-T1,fileC_1_file_1_g16265-T1,gene-LOC127006994-T1,file_1_file_1_g5026-T1,g63648-T1,gP30322-T1,gene-LOC123517976-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 106.fasta
proteinortho_grab_proteins.pl -exact 'gB5488-T1,Chr_9_Csap_01449-T1,gene-GWK47_025883-T1,fileC_1_file_1_g15430-T1,gene-LOC126998785-T1,file_1_file_1_g10238-T1,g137306-T1,gP76391-T1,gene-LOC123519051-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 107.fasta
proteinortho_grab_proteins.pl -exact 'gB45325-T1,Chr_9_Csap_08357-T1,gene-GWK47_053792-T1,fileC_1_file_1_g21993-T1,gene-LOC126989421-T1,file_1_file_1_g32972-T1,g82321-T1,gP35117-T1,gene-LOC123513988-T2' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 108.fasta
proteinortho_grab_proteins.pl -exact 'gB58429-T2,Chr_9_Csap_05417-T1,gene-GWK47_015652-T1,fileC_1_file_1_g28452-T1,gene-LOC127005797-T1,file_1_file_1_g4610-T1,g97486-T1,gP65249-T1,gene-LOC123517515-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 109.fasta
proteinortho_grab_proteins.pl -exact 'gB25681-T1,Chr_9_Csap_01720-T1,gene-GWK47_050520-T1,fileC_1_file_1_g26843-T1,gene-LOC127001764-T1,file_1_file_1_g21399-T1,g43112-T3,gP10737-T1,gene-LOC123505564-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 110.fasta
proteinortho_grab_proteins.pl -exact 'gB41524-T1,Chr_9_Csap_11202-T1,gene-GWK47_054761-T1,fileC_1_file_1_g42609-T1,gene-LOC126984430-T1,file_1_file_1_g3577-T1,g66768-T1,gP62588-T1,gene-LOC123506654-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 111.fasta
proteinortho_grab_proteins.pl -exact 'gB59583-T2,Chr_9_Csap_06383-T1,gene-GWK47_008980-T1,fileC_1_file_1_g17481-T1,gene-LOC127009585-T3,file_1_file_1_g2374-T1,g76115-T2,gP84251-T1,gene-LOC123519867-T3' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 112.fasta
proteinortho_grab_proteins.pl -exact 'gB96322-T1,Chr_9_Csap_09711-T1,gene-GWK47_026490-T1,fileC_1_file_1_g22331-T1,gene-LOC126986635-T1,file_1_file_1_g9198-T1,g53902-T1,gP76336-T1,gene-LOC123498799-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 113.fasta
proteinortho_grab_proteins.pl -exact 'gB86469-T1,Chr_9_Csap_23280-T1,gene-GWK47_014438-T1,fileC_1_file_1_g20003-T1,gene-LOC126984447-T4,file_1_file_1_g9021-T1,g39145-T1,gP20333-T1,gene-LOC123513074-T1' Panulirus_ornatus_ornatus.faa Birgus_latro.faa Paralithodes_camtschaticus_Paralithodes_camtschaticus.faa Eriocheir_sinensis_Eriocheir.faa Cinc.faa Mani.faa Portunus_trituberculatus_Portunus.faa Callinectes_sapidus_Callinectes.faa Chionoecetes_opilio_Chionoecetes.faa > 114.fasta
# sorted.species.list (for sequence headers)
#>Callinectes sapidus
#>Petrolisthes cinctipes
#>Petrolisthes manimaculis
#>Panulirus ornatus
#>Birgus latro
#>Paralithodes camtschaticus
#>Chionoecetes opilio
#>Portunus trituberculatus
#>Eriocheir sinensis
# sort sequences by header and replace header with species name
for fasta in *.fasta
do
paste -d'\n' sorted.species.list <(awk 'NR%2==0' <(bioawk -c fastx '{print}' $fasta | sort -k1,1V | awk '{print ">"$1;print $2}')) > $fasta.sorted.fasta
done
# concatenate all SCOs and align them
#seqkit concat *sorted.fasta | sed -e 's/\|.*$//' > sorted.concat.fasta
cut -f1 -d "-" *.sorted.fasta | awk -v RS=">" -v FS="\n" -v OFS="\n" '{for(i=2; i<=NF; i++) {seq[$1] = seq[$1]$i}}; END {for(id in seq){print ">"id, seq[id]}}' > sorted.concat.fasta
mafft --anysymbol --quiet sorted.concat.fasta > sorted.concat.mafft.fasta
# infer phylogeny
iqtree2 -s sorted.concat.trimal.phylip -nt AUTO -ntmax 6 -seed 12345 -bb 1000 -o "Panulirus_ornatus"