gabaldonlab / evolclust Goto Github PK

Hi!
I am trying to use Evolclust to analyze the conservation of several pairs of genes in bacteria, however I am having trouble understanding the process of obtaining the two required input files: .fasta file containing a list of proteins and .cml file containing information about homologous protein families.

Thank you very much in advance!

Hi Marina，
I try to run some of my own data with EvolCluster， everything was ok when I use testdataset：
python evolclust.py -i test_dataset.mcl -f test_dataset.fa -d evol_test --local

but when I use my own data ，Some errors occurred， It seems to be about mcl：
nohup: ignoring input
STEP1: Create initial files
STEP2: Calculate thresholds and obtain pairwise clusters (This can take a long time)
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STEP3: Filter paiwise clusters
[mclxIOstreamIn] no assignments yield void/empty matrix
[mcl] new tab created
___ [mclAlgorithmStart] attempting to cluster the void
[mcl] pid 58733
ite chaos time hom(avg,lo,hi) m-ie m-ex i-ex fmv
1 0.00 0.00 0.00/340282346638528859811704183484516925440.00/0.00 0.00 0.00 0.00 -2147483648
[mcl] jury pruning marks: <100,100,100>, out of 100
[mcl] jury pruning synopsis: <100.0 or really really really good> (cf -scheme, -do log)
[mcl] output is in out.mcl_list.txt.I20
[mcl] 0 clusters found
[mcl] output is in out.mcl_list.txt.I20

I'm checking what's wrong. Maybe you can give me some suggestions?

Hi, I see that the tools you developed are mainly used to search for gene clusters in eukaryotes, but bacterial genomes are relatively simpler and do not have introns. Can they be adjusted specifically for prokaryotic genomes?