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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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* [proteinortho-graph/blast-graph → species summary table](#proteinortho_history) (proteinortho_history.pl)
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[Internal programs](#internal-programs)
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... | ... | @@ -209,6 +210,112 @@ Reads Proteinortho outfile and its source fasta files to determin entries which |
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---
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<br>
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<h3>proteinortho-graph/blast-graph → species summary table</h3>
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how are the species connected given the proteinortho-graph/blast-graph
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tool: **proteinortho_history.pl**
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```
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proteinortho_summary.pl produces a summary on species level.
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SYNOPSIS
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proteinortho_summary.pl (options) GRAPH (GRAPH2)
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GRAPH Path to the *.proteinortho-graph or *.blast-graph file generated by proteinortho.
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GRAPH2 (optional) If you provide a blast-graph AND a proteinortho-graph, the difference is calculated (GRAPH - GRAPH2)
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Note: The *.proteinortho.tsv file does not work here (use the proteinortho-graph file)
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OPTIONS
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-format,-f enables the table formatting instead of the plain csv output.
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```
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<details>
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<summary>More details and examples (Click to expand)</summary>
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```
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$ proteinortho test/*faa
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$ proteinortho_summary.pl myproject.proteinortho-graph
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# The adjacency matrix, the number of edges between 2 species
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# file C.faa C2.faa E.faa L.faa M.faa
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C.faa 0 1 13 18 16
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C2.faa 1 0 1 1 1
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E.faa 13 1 0 14 15
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L.faa 18 1 14 0 42
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M.faa 16 1 15 42 0
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# file average number of edges
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C.faa 9.6
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C2.faa 0.8
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E.faa 8.6
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L.faa 15
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M.faa 14.8
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# The 2-path matrix, the number of paths between 2 species of length 2
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# file C.faa C2.faa E.faa L.faa M.faa
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C.faa(0) 750 47 493 855 952
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C2.faa(1) 94 4 42 74 73
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E.faa(2) 986 84 591 865 797
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L.faa(3) 1710 148 1730 2285 499
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M.faa(4) 1904 146 1594 998 2246
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# file average number of 2-paths
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C.faa(0) 1088.8
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C2.faa(1) 95.2
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E.faa(2) 997
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L.faa(3) 1374.2
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M.faa(4) 1377.6
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```
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</details>
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<details>
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<summary>More details and examples (Click to expand)</summary>
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```
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$ proteinortho test/*faa
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$ proteinortho_summary.pl myproject.proteinortho-graph myproject.blast-graph
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# The adjacency matrix, the number of edges between 2 species
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# file C.faa C2.faa E.faa L.faa M.faa
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C.faa 0 0 -3 -2 -5
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C2.faa 0 0 0 0 0
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E.faa -3 0 0 -4 -8
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L.faa -2 0 -4 0 -3
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M.faa -5 0 -8 -3 0
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# file average number of edges
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C.faa -2
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C2.faa 0
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E.faa -3
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L.faa -1.8
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M.faa -3.2
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# The 2-path matrix, the number of paths between 2 species of length 2
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# file C.faa C2.faa E.faa L.faa M.faa
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C.faa(0) 38 0 48 27 30
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C2.faa(1) 0 0 0 0 0
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E.faa(2) 96 0 89 30 27
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L.faa(3) 54 0 60 29 42
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M.faa(4) 60 0 54 84 98
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# file average number of 2-paths
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C.faa(0) 49.6
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C2.faa(1) 0
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E.faa(2) 59.8
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L.faa(3) 45.4
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M.faa(4) 59.2
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```
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</details>
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<br>
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---
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<br>
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<h1>Internal programs</h1>
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the following programs are used by proteinortho internaly.
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