A little pipeline that takes core_seq.txt and DATASET.xls files from BPGA The program splits the sequences in the core_seqfile by protein family, then, align (muscle), trim (Gblocks), filter out the aligments with no sequences after trimming.
The processed alignments are then concatenated into a supermatrix (FasConCat), which is labelled with the taxon names. The partition file for IQ tree is prepared and then the supermatrix and the partition file are used to contruct a phylogeny (IQtree) with independent model per partitions.
Dependecies:
muscle (aligner):
https://www.drive5.com/muscle/ Install like this (install in /bin):
sudo apt-get install muscle
GBlocks (trimmer):
http://molevol.cmima.csic.es/castresana/Gblocks.html http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html#Installation
Install like this (install in /bin):
wget http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z
tar xvf Gblocks_Linux64_0.91b.tar.Z
cd Gblocks_0.91b/
sudo mv Gblocks /usr/bin/
fastconcat (Concatenation of alignments): Install like this (put it in the same folder as your inputs):
wget https://github.com/PatrickKueck/FASconCAT/raw/master/FASconCAT_v1.11.pl
Running this script
perl core_to_phylo.pl core_seq.txt DATASET.xls
Inputs are obtained from a succesful run of BPGA https://iicb.res.in/bpga/
core_seq.txt is under /Sequences
DATASET.xls is undet /Supporting_files
Common issue: You may have opened and saed the input files in windows or something other than a unix OS clean the files with dos2unix (sudo apt-get install dos2unix)
dos2unix DATASET.xls
dos2unix core_seq.txt
Try again