This is a pipeline that can be used to generate a phylogenetic tree, including a heatmap showing carriage of specific genes, the assigned phylogroup of each strain, and the names of each strain. It should now be capable of working with any sort of strains - currently I'm working on making small improvements.
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Possible SED issue with Windows 11 (Ubuntu on terminal) #7
There's the possibility that running PhyloGenes on a Windows 11 (or perhaps 10) terminal using Ubuntu it may return a SED error - if this occurs, the fix is to go into the script for PhyloGenes.sh and change line 163 from:
sed '/^>/ s/^.*gene=\([Aa-Zz]\+\).*/\1/' Z_Orthologs.txt | sed '1~2s/^/>/' > $genesForTree/geneList.txt
to:
sed '/^>/ s/^.*gene=\([A-z]\+\)].*/\1/' Z_Orthologs.txt | sed '1~2s/^/>/' > $genesForTree/geneList.txt
And it should work fine. Remember to alter the line back to the original if switching to anything other than Windows Terminal.
There's the possibility that running PhyloGenes on a Windows 11 (or perhaps 10) terminal using Ubuntu it may return a SED error - if this occurs, the fix is to go into the script for PhyloGenes.sh and change line 163 from:
sed '/^>/ s/^.*gene=\([Aa-Zz]\+\).*/\1/' Z_Orthologs.txt | sed '1~2s/^/>/' > $genesForTree/geneList.txtto:
sed '/^>/ s/^.*gene=\([A-z]\+\)].*/\1/' Z_Orthologs.txt | sed '1~2s/^/>/' > $genesForTree/geneList.txtAnd it should work fine. Remember to alter the line back to the original if switching to anything other than Windows Terminal.