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# Table of Contents
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[Conversion Tools](#conversion-tools)
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* [proteinortho.tsv → html](#proteinorthotsv-html) proteinortho2html.pl
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* [proteinortho.tsv → OrthoXML](#proteinorthotsv-orthoxml) proteinortho2xml.pl
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* [proteinortho.tsv → tree (newick format)](#proteinorthotsv-tree-newick-format) proteinortho2tree.pl
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* [proteinortho.tsv → html](#proteinorthotsv-html) (proteinortho2html.pl)
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* [proteinortho.tsv → OrthoXML](#proteinorthotsv-orthoxml) (proteinortho2xml.pl)
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* [proteinortho.tsv → tree (newick format)](#proteinorthotsv-tree-newick-format) (proteinortho2tree.pl)
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[Extract Results](#extract-results)
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* [protein ids/names or proteinortho.tsv → extract protein-sequences (fasta)](#protein-idsnames-or-proteinorthotsv-extract-protein-sequences-fasta) proteinortho_grab_proteins.pl
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* [protein id/name → history](#protein-idname-history) proteinortho_history.pl
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* [two proteinortho-graph files → difference](#two-proteinortho-graph-files-difference) proteinortho_compareProteinorthoGraphs.pl
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* [proteinortho.tsv → singletons](#proteinorthotsv-singletons) proteinortho_singltons.pl
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* [protein ids/names or proteinortho.tsv → extract protein-sequences (fasta)](#protein-idsnames-or-proteinorthotsv-extract-protein-sequences-fasta) (proteinortho_grab_proteins.pl)
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* [protein id/name → history](#protein-idname-history) (proteinortho_history.pl)
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* [two proteinortho-graph files → difference](#two-proteinortho-graph-files-difference) (proteinortho_compareProteinorthoGraphs.pl)
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* [proteinortho.tsv → singletons](#proteinorthotsv-singletons) (proteinortho_singltons.pl)
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[Internal programs](#internal-programs)
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---
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---
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<h1>Conversion Tools</h1>
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<h3>proteinortho.tsv → html</h3>
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... | ... | @@ -23,6 +28,7 @@ Any further (optional) files should be fasta files, for conversion of the identi |
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The HTML output is printed to stdout, use '>' to write the html output to a file.
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```
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<br>
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---
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<br>
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... | ... | @@ -37,6 +43,7 @@ Reads Proteinortho file (not proteinortho-graph file!) and produces the OrthoXML |
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for more information about the OrthoXML format see [orthoxml.org](http://www.orthoxml.org/xml/Main.html)
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<br>
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---
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<br>
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... | ... | @@ -51,6 +58,7 @@ output: corresponding UPGMA tree in newick format |
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options: -o=[FILE] prints output to the given file rather than STDOUT
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```
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<br>
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---
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<br>
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... | ... | @@ -130,6 +138,7 @@ DESCRIPTION |
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</details>
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<br>
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---
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<br>
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... | ... | @@ -160,6 +169,7 @@ proteinortho_history.pl (-project=myproject) QUERY (FASTA1 FASTA2 ...) |
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NOTE: if you use the -keep option and you have the project_cache_proteinortho/ directory, this program additionally searches for all blast hits.
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```
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<br>
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---
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<br>
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... | ... | @@ -175,6 +185,7 @@ Compares two Proteinortho-graph files and reports additional and different entry |
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O = only here
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```
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<br>
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---
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<br>
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... | ... | @@ -187,6 +198,7 @@ proteinortho_singletons.pl FASTA1 FASTA2 FASTAN <PROTEINORTHO_OUTFILE |
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Reads Proteinortho outfile and its source fasta files to determin entries which occure once only
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```
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<br>
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---
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<br>
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... | ... | |