How to write to a newick tree with root?

[teng-gao]

Currently, using cas_tree.get_newick() I get a tree that, when read into R as a phylo object, is unrooted (example below).

Is there a way to add a root in the written newick tree?

'((((((((((GCTAGTGTCCTCATCA,(GCTAGCTCAGTCTAAT,TGTCAATCAGAGGCTA)),TGGTGATTCTGGCATG,TCGCGAGGTGTGTGGT),(GCGATTTAGCCTCTGT,GTACTAATCCGGTATG)),(((ATCACAATCCATCAGG,GTTTCAGCACAAGCCT),GGTGTGACAAACGGGC),GGATATTGTCATGCAA,(TGCATCCTCAAGCGCC,TTATAGCCAGAGAGCC),(ATCTTTGGTCTTGCAT,TCGTTATTCGACAAAG),AACTGTTCACTAGCGT,GGTTCTTGTATGTGGC,(CGGTGAACATGTTGGC,GCCCAAATCAATTACG)),CAGGCTATCCTAAGTA,(AATAACCGTAGTTACG,TGTTGGCCACGGTACT),(((ACGGTTTAGACACCGC,AAACCGAAGTTTGAGC),(TCCATATTCGCCTAAG,(GTCATTAAGTTAGCTA,CGGCCATAGACAGGTA))),(TCAAGACTCTGCAAAC,CAGGAAGGTAAAGCAA),CCTAAGTAGTAGAGGC,((AATACCGGTTCCTGTG,TTTGCGGAGCTCCCTG),((GTCCGTAAGAAAGGAA,(GTGCGGTTCACGTTAA,GGGTTTGTCACTCGCT)),(CGCTTAACACGAATCC,TACGTTAAGGGTCCAC))))),(AACTTAGTCGTGCCTT,TAGCAGGCAGATTCAT)),(AGCAATACAGGTTCAC,(CAATGTCAGTTAGACC,AGGACTAAGGCGTAAA))),(AATCCTAAGGAACACA,ATTACTGAGTCACCTC)),(AATAGAGGTTCGGGAT,CCATAATCATGGCCCA),(GGCATGGAGCAGCTAT,GCACGAACATTGTGGC)),(((ACAGTATGTCATCATC,TACAGCTAGTGAACCT),AGCCTAAGTTGGTTAG),((GGTTACCCACCACAAC,GCCACTAAGAATGACG),CGTGTTACAGGAAGCC))),(((((((TACTCAAAGAGCAAGC,ACTTATGAGTCATTAG),(AGTGTTTCAGCACGTT,TCGTTACGTGTCCAGG),((CTTCAAGCAAGCCACT,CTAATCCGTTGCGTAA),(CATAGCTAGCCTGGTA,CTCCGGACATTGTGTG),(TTTCACCCAGGAAGCC,GAGGTTAAGCAAGGGT,CGTGGTTCAAGGTACG,TGTCCTGGTGTTGCAA,GAGTCATTCACTTCAT,(AATACCGGTTTCGCGC,(CCAAGTTAGCTGGCTA,TGCGCGAGTTCCGGGA)),GGAGCAAGTTCCTCCT,CGCATATAGCACTAGT,(AGTATAGCACTTAACG,CAAACTGGTTAGGCGT,CTGACATAGTGCACGC,GTAGGTGCATCCAGGT,GTTCGCGCAATTGACT))),(TTTAACCTCTATCGCC,TGCAGGCTCATTGACA)),(CTACGAAGTCATTACC,TTGCAATCAGTACCGT)),(GAGGAGGCAGTTATCG,(GGTATTTCAACGTGCT,CTTCAGGAGTAGCGGG))),TACGCACCAACTAGAA),((GCATGAAAGATGGAGC,GACCTGATCCCGTTGT),(AGCCTGGGTTTGAGGC,(GCTGCAATCGCTTCTA,(GTGAATCTCGTTAAGC,(GTGCACGGTTAAGCCA,GTAGGAGGTTCCGCAC)))))),(((((((((CGAATATGTAATTAGC,TGCTCCGTCGGGCCAT),GGTGCTGGTTGCGCGA),(AGTGCCGGTATTGTCC,CAGGACCTCGCTAGCA)),((TTGTCCCAGGAATAAC,CGTCCTAGTCTTACTA),(GTGATGAAGGGCCACT,AGTAACGAGTCCTGAG))),GGTCAAGCAACACTTG),(((CGCAATGTCTATTGTC,GCCTTAACAGCCAGTT),TACATCAAGTGCACGC),TTTAGCTTCATGTGGT)),((AGCAAATAGGTTTGAC,TAGTCAATCAGAAACG),(TGTAACTCACATAACT,GGTTGCTCAGTTATCG))),(GATTGATGTCCGTGAG,CATCCTCAGTTATGTG)),CTCTAGCTCCTTCAAT),(CCTATATTCTTGCTAT,(TTAGCGGTCCGCAAAT,AAGCTCCCAAGGTGCA)),AATGAAGGTTAGTTGG,(TGGAACAAGTGAGGTA,(TGGACGGAGGAACCGG,(GCTAAGTTCAATCTCT,ATCTTTGGTAATGGAA)))),((((((((CTTACCGGTCCACAAA,TGAAGTGAGCTATGAC,GAGAAACGTGGACATC),((GCTAACAGTTGCACGG,ACTTGAATCTTTAGGA),(CCTAATAAGGCAGGTG,TGAGAACCAAGGTACG,TTTGTCCCATCCCGCT))),(((GAGGCTACAACCTGGT,(AATTGGGAGTAACCCG,CCGATGCAGTATCGCG)),(GACCTCAAGGAGGACT,(GCGGAACCAGGTCCTG,GAAAGCCAGGGCTTTG,ACTTACAAGGCGCACT,CATCCTGGTGATCAGC,CTGGCTAAGACACCGC,CTGTTGGAGGTTACAC,GACCTTTGTGTGTGGT,GCTTTGTGTAGGTTAT,TCTCACCAGTTTGGGT,TCTCCTCGTCAAAGGG,TGACTTCGTTGCTTCG,TGGTCAAGTAGTAAGA,TTTATGGAGGACACTT))),(TGGCCTGCAGCTACGT,(GGTTAGCGTCCTTTAA,ATGGCTTAGCATGACT)))),(ATATGGTGTAACGAGG,TTGCACACAATGCCTA)),(CGTTGCAAGGCTAAGA,GGGTATTTCGATATTG)),TTGGGCCAGCTAAGTC),AGTTGTCAGCTTAGCG),(GGAGCAAGTGCGCGTA,ATTACGTCAAACTGCC)),((((GTAGGTGCACCCTCAC,GGAATCTTCGGGACCT),TAGTTGTCACGTGCTG,TGCGCAGGTTAGCAGC),(GCTGATCCAGTAATAG,(CAGCTATAGCTCGCTT,TAGCGCGGTTTCCTCC)),((TATGGTCAGGTCCTGA,ATTACTGAGCAGGCCT),(GGGCAATAGCGCATTG,TGTTTGTTCTAATCCT))),((TTGCGAGTCGGTTAGT,CATGCATAGAGGGACT),(TGCTTCCAGGGACGCA,GGTATTGGTTTCAGGA)),((GTGCTGATCACTCGCT,(CGTGCTGCAGCATGAG,GCACCTAAGGCATTAC)),GCAATGAAGCCTGACA)),((((((GCTTCGCGTTTAGTCC,GCCAATAGTTAAGTGT),((GGTCATTAGTTAGCTA,GTTAGGCGTTCGCTCA),GGCCTTCGTACAAAGA,(GGAAGCTAGCGAGTAA,GCAGGCTTCATGGTTA,TTAATCGAGCTCGCTT,(GCCTATTGTTAGGCGT,GCGGTTGGTTCCTGAT)))),(GTTCGCTTCCGGCTAA,CGGTAACGTGAGCGAA)),TGGCTTTGTCACGAAC),GTCAAACTCATAATCG),CCTAAGTAGAAGGTGC),((((((GGCTATGTCATTTGCT,TGCCTGTTCGGGCCAT),(AAAGGACGTAGCTAGC,TACGTTAAGCTGAGGG)),(GCTGAGGAGTAACGGA,AGCTCATAGCTTACTT)),(TGCTTAAAGCATCCAG,GCCAATTAGCTCGCTT)),((ATGTTCAAGTAACAGG,GCGATTAGTCATCATC),GTGTCCAAGCATTATG)),CATAACGGTAGGTTTG),((TAATCACCAACAACAA,(CAGCTATAGGCCAATT,TTCGTGCTCATGCAAC)),(GACTATTCATTAGCGC,ATTGCGCCAACTCGCG)),(((TGGCCAATCATGTGGT,GCTTAACAGGATTGAG),GCGCCTTGTTGAGCCG),(TAGCTAATCAGCTAAC,AGTTACATCGTTACTT)));'

[mattjones315]

Hey @teng-gao,

Can you give me a bit more information on this tree? Is it rooted in Cassiopeia, just not when you write out to newick? What happens if you add a "dummy" node to the very front of the newick string? What package are you using to read into R?

Hope to get this solved for you soon,
Matt