Publication date
July 2019
DOIAbstract
adding small compensation if any white space after accessions in ncbi accessions input file changing 'GToTree-gen-iToL-map' to 'gtt-gen-itol-map
adding small compensation if any white space after accessions in ncbi accessions input file changing 'GToTree-gen-iToL-map' to 'gtt-gen-itol-map
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
small fix to handle mapping file -m properly when user provides paths to input files in first column...
adding additional-target pfam search option to main program and creating iToL-compatible files for e...
better checking and error message improvement when input accessions file format has problems, and wh...
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
adding gtt-update-ncbi-taxonomy helper script to be able to easily keep the db up-to-date for use wi...
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizin...
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxo...
added gtt-gen-SCG-HMMs to be able to generate new SCG-sets the same way those packaged with GToTree ...
expanded functionality of gtt-subset-GTDB-accessions to now be able to select 1 random representativ...
added in check for special characters in user-provided mapping file, re: https://github.com/Astrobio...
added checks for duplicates, tabs, and/or spaces in input fasta, amino-acid, and genbank main file
added checks for duplicates, tabs, and/or spaces in input fasta, amino-acid, and genbank main file
fixed missing options/code for subsetting based on arbitrary rank with gtt-subset-GTDB-accessions, r...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
small fix to handle mapping file -m properly when user provides paths to input files in first column...
adding additional-target pfam search option to main program and creating iToL-compatible files for e...
better checking and error message improvement when input accessions file format has problems, and wh...
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
adding gtt-update-ncbi-taxonomy helper script to be able to easily keep the db up-to-date for use wi...
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizin...
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxo...
added gtt-gen-SCG-HMMs to be able to generate new SCG-sets the same way those packaged with GToTree ...
expanded functionality of gtt-subset-GTDB-accessions to now be able to select 1 random representativ...
added in check for special characters in user-provided mapping file, re: https://github.com/Astrobio...
added checks for duplicates, tabs, and/or spaces in input fasta, amino-acid, and genbank main file
added checks for duplicates, tabs, and/or spaces in input fasta, amino-acid, and genbank main file
fixed missing options/code for subsetting based on arbitrary rank with gtt-subset-GTDB-accessions, r...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
small fix to handle mapping file -m properly when user provides paths to input files in first column...
adding additional-target pfam search option to main program and creating iToL-compatible files for e...
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