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1 | 1 | # read2tree
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2 | 2 |
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3 |
| -read2tree is a software tool that allows to obtain alignment matrices for tree inference. For this purpose it makes use of the OMA database and a set of reads. Its strength lies in the fact that it bipasses the several standard steps when obtaining such a matrix in regular analysis. These steps are read filtereing, assembly, gene prediction, gene annotation, all vs all comparison, orthology prediction, alignment and concatenation. |
| 3 | +read2tree is a software tool that allows obtaining alignment matrices for tree inference. For this purpose it makes use of the OMA database and a set of reads. Its strength lies in the fact that it bypasses the several standard steps when obtaining such a matrix in regular analysis. These steps are read filtering, assembly, gene prediction, gene annotation, all vs all comparison, orthology prediction, alignment and concatenation. |
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5 | 5 | read2tree works in linux with [](https://www.python.org/downloads/release/python-310/)
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6 | 6 |
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7 | 7 | ## New release
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8 |
| -We are now realasing Read2Tree v2.0.0 with improved spead and logging. As the aligner, we are now using minimap2 [minimap2](https://github.com/lh3/minimap2). Also, MAFFT and IQtree are now using multiple threads. We would suggest to run r2t with `--debug` which helps to debug later. Please note that arguments have slightly changed in this release(see below for details). |
| 8 | +We are now releasing Read2Tree v2.0.0 with improved speed and logging. As the aligner, we are now using minimap2 [minimap2](https://github.com/lh3/minimap2). Also, MAFFT and IQtree are now using multiple threads. We would suggest running r2t with `--debug` which helps to debug later. Please note that arguments have slightly changed in this release(see below for details). |
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10 | 10 |
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11 | 11 | ## Read2Tree Talk:
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@@ -45,7 +45,7 @@ conda install -c conda-forge biopython numpy Cython ete3 lxml tqdm scipy pyparsi
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45 | 45 | conda install -c bioconda dendropy pysam
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46 | 46 | ```
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47 | 47 |
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48 |
| -Besides, you need softwares including [mafft](http://mafft.cbrc.jp/alignment/software/) (multiple sequence aligner), [iqtree](http://www.iqtree.org/) (phylogenomic inference), [minimap2](https://github.com/lh3/minimap2) (long and short read mappers), and [samtools](http://www.htslib.org/download/) which could be installed using conda. |
| 48 | +Besides, you need software packages including [mafft](http://mafft.cbrc.jp/alignment/software/) (multiple sequence aligner), [iqtree](http://www.iqtree.org/) (phylogenomic inference), [minimap2](https://github.com/lh3/minimap2) (long and short read mappers), and [samtools](http://www.htslib.org/download/) which could be installed using conda. |
49 | 49 | For this version, the `--read_type` argument accepts any minimap2 options string that defines how reads are aligned to the reference. For example, it could be `-ax sr`, `-ax map-hifi` or `-ax map-ont`. You can also pass `--threads 40` to be used with minimap2.
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50 | 50 | ```
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51 | 51 | conda install -c bioconda mafft iqtree minimap2 samtools
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