Publication date
September 2020
DOIAbstract
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
fixing mistake in summary table reporting which genomes were retained in the final alignment Codebas...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
added checks for duplicates, tabs, and/or spaces in input fasta, amino-acid, and genbank main file
added in check for special characters in user-provided mapping file, re: https://github.com/Astrobio...
Check added by @vinisalazar looking for duplicates in user-provided mapping file, previously would r...
better checking and error message improvement when input accessions file format has problems, and wh...
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
added capability to start off with amino acid files of coding sequences as input improved handling o...
genbank and refseq assembly summary tables are now cached instead of downloaded every run (https://g...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
fix to slight miscalculation of estimated completeness when multiple gene-copies presen
adding small compensation if any white space after accessions in ncbi accessions input file changin...
enabled gzipped fasta files or genbank files to be provided as inputs added specific versions to con...
adding in faster alignment settings when working with >= 5000 genomes, and notice about it pointing ...
fixing mistake in summary table reporting which genomes were retained in the final alignment Codebas...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
added checks for duplicates, tabs, and/or spaces in input fasta, amino-acid, and genbank main file
added in check for special characters in user-provided mapping file, re: https://github.com/Astrobio...
Check added by @vinisalazar looking for duplicates in user-provided mapping file, previously would r...
better checking and error message improvement when input accessions file format has problems, and wh...
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
added capability to start off with amino acid files of coding sequences as input improved handling o...
genbank and refseq assembly summary tables are now cached instead of downloaded every run (https://g...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
fix to slight miscalculation of estimated completeness when multiple gene-copies presen
adding small compensation if any white space after accessions in ncbi accessions input file changin...
enabled gzipped fasta files or genbank files to be provided as inputs added specific versions to con...
adding in faster alignment settings when working with >= 5000 genomes, and notice about it pointing ...
fixing mistake in summary table reporting which genomes were retained in the final alignment Codebas...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
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