cgMLSA

phylogenetic analytic toolsets based on cgMLST

INSTALLATION:

cgMLSA was developed and tested in Python 3.8. cgMLSA depends on several Python libraries:

ete3
numba
numpy
pandas
click

All libraries can be installed using pip:

pip install ete3 numba numpy pandas click

EToKi also calls the following 3rd party programs for different pipelines:

Astral (v5.15.1)
ASTRID (v1.4)
blastn
diamond
erable
FastTreeMP
mafft
makeblastdb
rapidnj

All 3rd party programs need to be installed in the cgMLST/dependencies folder.

Quick Start (with examples)

Build multi-sequence alignments for every genes in the cgMLST scheme

python modules/01_alignAlleles.py -p examples/examples.profile.gz -n 10 --ublast -d examples/genes/ examples.examples.alleles.fasta.gz

Calculate nucleotide distances of genomes

python modules/02B_alleleAlign2GenomeDistance.py -o examples/examples.dist -p examples/examples.profile.gz -d examples/genes

Calculate allelic trees

python modules/03_getAlleleTrees.py -d examples/genes --raxml_ng

Add genomic labels into the gene trees

python modules/04_expendAlleleTree.py -d examples/genes -p examples/examples.profile.gz -o examples/examples.geneTrees

Calculate a guide_tree using ASTRID, and calculate posterior probabilities (PP) of branches using ASTRAL

python modules/05_summariseGeneTrees.py -i examples/examples.geneTrees -o examples/examples.guide_tree

Split the guide tree based on PP values

python modules/06_splitAstridTreeByQuartetSupport.py -i examples/examples.guide_tree -o examples/examples.subset -m 10 -x 20

Generate disjoint subsets of gene trees

python modules/07_generateSubtreesForEachGroup.py -g examples/examples.subset -i examples/examples.geneTrees -p examples/examples

Calculate ASTRAL trees for each disjoint subsets

python modules/08_runAstralForEachSubtrees.py -d examples

Generate the supertree by concatenating disjoint subtrees together

python modules/09_summarizeAstralSubtrees2SuperTree.py -d examples -o examples/examples.supertree

Update the branch lengths of the supertree based on genomic distances

python modules/10_reviseBranchLength.py -t examples/examples.supertree -g examples/examples.geneTrees -d examples/examples.dist -o examples/examples.species_tree

zheminzhou/cgMLSA