GToTree
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AstrobioMike
A user-friendly workflow for phylogenomics
it currently doesn't check for custom ones placed in the stored location and report them too, which would be helpful if it did
"Species", at least for NCBI, includes the genus too. So when specifying, e.g. `-L Genus,Species`, it adds the genus twice. I should put in something that accepts the input but...
right now, if a search for a species-level taxon is done, it will retain the space in the output file name, e.g.: `gtt-get-accessions-from-GTDB -t "Bacillus_A anthracis"` creates files like: `GTDB-Bacillus_A...
Hello! I recently discovered your GToTree and have found it super helpful for my master's project and your clear instillation and instructions have been a huge help in getting it...
I want to use my newly assembled bacterial genomes with some reference genomes to generate a phylogeny tree. I found your tool very interesting. I am using a singularity container...
Hi, I thought you might like a feedback post for the SCG generator script vs the wiki instruction. I just finished running a test run of the gtt-gen-SCG-HMMs script versus...
Hi Mike, I was planning to build very larger trees via fasttree2 option but I found that for most recent AMD and Intel CPUs, SIMD version of fasttree2, which is...
Thanks so much for your continued work on this really helpful workflow, @AstrobioMike ! I have a feature request (so low priority) regarding GToTree. Currently, if a list of NCBI...
Hi Mike, I'm a PhD student in Laura Hug's lab currently working on a side project related to constructing universal ToLs. I was following your ToL example using the universal...
I'm trying to build a custom SCG set using GToTree's built in SCG screening tool (which usually works wonderfully by the way). Right now I'm getting "Downloading the PFam HMM...