TreeSAPP
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hallamlab
A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
Bumps [joblib](https://github.com/joblib/joblib) from 1.0.0 to 1.2.0. Changelog Sourced from joblib's changelog. Release 1.2.0 Fix a security issue where eval(pre_dispatch) could potentially run arbitrary code. Now only basic numerics are supported....
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Hello! I am a master student in evolutionary biology trying to run treesapp assign on a fasta file containing 11 a.a sequences for the mitochondrial gene ATPase6 (and have tried...
Taxonomic classification is reliant on the evolutionary distance (i.e. branch-length, or number of substitutions) linear model. Distances between query sequences and reference sequences inferred during phylogenetic placement are influenced by...
[ClipKIT](https://github.com/JLSteenwyk/ClipKIT) is a new MSA-trimming Python package. The authors indicate the trimmed MSAs generated by ClipKIT are more "desireable" (combined RF distance and bipartition supports) than those from competing tools,...
**Is your feature request related to a problem? Please describe.** A user, Aditi Nagaraj, found a series of ORFs predicted by Prodigal (within `treesapp assign`) that had fragmented a single...
I'm getting error when running this command `treesapp assign -i /Users/melody/graftM/1_RAWDATA/BO45_S2_L001_R1_001.fastq --refpkg_dir /Users/melody/TreeSAPP/RefPkgs/Methanogenesis/McrA/IMG_Archaeal_MAGs_update/final_outputs -o /Users/melody/TreeSAPP/TreeSAPP_McrA_IMG -v -n 8` but it's working when running with `treesapp assign -i /Users/melody/graftM/1_RAWDATA/BO45_S2_L001_R1_001.fastq -t McrA...
`treesapp abundance` calculates TPM or FPKM for entire query sequences. The depth of coverage, however, is unknown. A new feature that reports the pile-up along each query sequence's length would...
`treesapp purity` is (mostly) good at indicating whether reference packages will end up classifying off-target homologs. A missing piece, however, leaves users unsure of what to do with the reference...
`treesapp purity` calls `treesapp assign` to classify the reference sequences. The warning and error messages are verbose in each, but if there is an error in `treesapp assign` the exact...