PhaME
PhaME copied to clipboard
LANL-Bioinformatics
Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes...
Hello, what is this option, not explained anywhere... looks like a threshold to call SNPs, but what is the permitted range and what it means? like 0.6 what does it...
This issue is similar to, but distinct from issue #11. I have installed PhaME via conda and when I attempt to execute it, I get: `[13:18:16] Need samtools --version >=...
Dear devs, Ive run into an small issue, but have no clue how to solve it. So when I start a run I get this message: `Need samtools --version >=...
Hi, I'm getting this error and seems like an project_all_alignment.fna file is not generated. error logs below: [22:46:43] Checking version: samtools --version is >= 1.3 - ok, have 1.14 [22:46:43]...
Hello, I have installed `phame` using the first conda installation method, and I see that in the produced `____.error` file there are several errors. 1. error running get_repeat_coords.pl -l 75...
I have successfully installed Phame on my Desktop computer through conda (Ubuntu 16.04 64 bit OS; 8 GB RAM, Core i7 processor). I had ran the test files successfully, however...
Hello, I have an Issue with Phame that is difficult to overcome. We succed to solve the issues with Samtools but when I run the tools, I have phylogenetical trees...
So I have installed phame and the dependencies separately in a new environment and installed phame by cloning the github version, as recommended in another thread. When I run the...
What does the "buildSNPdb = 1" actually do? Not sure whether this has been asked before. I am running an analysis with reads from 300 _Vibrio cholerae_ isolates, and in...
Would be nice if the pipeline was optimised to work with compressed files.
Metadata
Owner
Metadata
Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes...