Now default mode is to use only genes found in single-copy in a given genome, unless "best-hit mode" is specified with the "-B" flag. See here for more info: Main output genome summary table includes two new columns: if that genome made it to the final tree, and if so, how many target genes it contributed to the final alignment minor bug fixes Codebase: https://github.com/AstrobioMike/GToTree Documentation: https://github.com/AstrobioMike/GToTree/wik
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
updating gtt-get-accessions-from-GTDB https://github.com/AstrobioMike/GToTree/commit/bbaec5893342e05...
This release fixes minor bugs and adds critical new functionality to generate an automatically filte...
fixing mistake in summary table reporting which genomes were retained in the final alignment Codebas...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
More posix compatibility fixes Added output table of hit-counts per target-gene per genome Codebase:...
fix to label swapping when mapping file specified an append only (column 3 present, but column 2 emp...
adding in faster alignment settings when working with >= 5000 genomes, and notice about it pointing ...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
fix to slight miscalculation of estimated completeness when multiple gene-copies presen
small, but important fix to rarely used -X parameter that was introduced in release 1.6.20 this is o...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
genbank and refseq assembly summary tables are now cached instead of downloaded every run (https://g...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
expanded functionality of gtt-subset-GTDB-accessions to now be able to select 1 random representativ...
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
updating gtt-get-accessions-from-GTDB https://github.com/AstrobioMike/GToTree/commit/bbaec5893342e05...
This release fixes minor bugs and adds critical new functionality to generate an automatically filte...
fixing mistake in summary table reporting which genomes were retained in the final alignment Codebas...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
More posix compatibility fixes Added output table of hit-counts per target-gene per genome Codebase:...
fix to label swapping when mapping file specified an append only (column 3 present, but column 2 emp...
adding in faster alignment settings when working with >= 5000 genomes, and notice about it pointing ...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
fix to slight miscalculation of estimated completeness when multiple gene-copies presen
small, but important fix to rarely used -X parameter that was introduced in release 1.6.20 this is o...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
genbank and refseq assembly summary tables are now cached instead of downloaded every run (https://g...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
expanded functionality of gtt-subset-GTDB-accessions to now be able to select 1 random representativ...
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
updating gtt-get-accessions-from-GTDB https://github.com/AstrobioMike/GToTree/commit/bbaec5893342e05...
This release fixes minor bugs and adds critical new functionality to generate an automatically filte...
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