Mercurial > repos > oinizan > frogs
diff tree.xml @ 21:74a9b83110a7 draft
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
| author | oinizan |
|---|---|
| date | Thu, 30 Mar 2023 06:09:01 +0000 |
| parents | 4dd70eba5941 |
| children | 57824202c333 |
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--- a/tree.xml Fri Mar 10 14:03:08 2023 +0000 +++ b/tree.xml Thu Mar 30 06:09:01 2023 +0000 @@ -52,7 +52,7 @@ What it does -This tool creates a multiple alignment of OTUs with `Mafft <http://mafft.cbrc.jp/alignment/software>`_. +This tool creates a multiple alignment of ASVs with `Mafft <http://mafft.cbrc.jp/alignment/software>`_. And creates a rooted phylogenetic tree with `FastTree <http://www.microbesonline.org/fasttree/>`_ and `Phangorn R package <https://cran.r-project.org/web/packages/phangorn/index.html>`_. .. class:: infomark page-header h2 @@ -65,14 +65,14 @@ **Fasta file**: -The OTU sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). +The ASV sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). Careful: FROGS Tree works only with less than 10 000 sequences! .. image:: FROGS_tree_otufile.png **Biom file**: -The OTUs biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). +The ASVs biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). This file can be obtained in particular with the FROGS pipeline. .. class:: h3 @@ -87,7 +87,7 @@ **Report file** (report.html): -The report file describing which OTUs are contained or not in the phylogenetic tree. +The report file describing which ASVs are contained or not in the phylogenetic tree. .. class:: infomark page-header h2