Allow genome names longer than 7 characters to be output in matrix files
Made extend anchors more robust, allowed fewer CGNs for ends of contigs, reduced window sizes, and some other minor stuff
MODIFIED: create_meta_groupings.pl - touched up pod in help documentation for clarity/formatting
MODIFIED: parse_genbank_files.pl - changed name...
Revamped printing of genome list file for check...
MODIFIED: ftp_download_ncbi_annotation.pl - imp...
MODIFIED: parse_genbank_files.pl - slightly bet...
MODIFIED: parse_genbank_files.pl - now checks t...
MODIFIED: parse_genbank_files.pl - new option '...
MODIFIED: ftp_download_ncbi_annotation.pl - now...
MODIFIED: parse_genbank_files.pl - now calls do...
MODIFIED: ftp_download_ncbi_annotation.pl - now...
MODIFIED: ftp_download_ncbi_annotation.pl - no ...
MODIFIED: ftp_download_ncbi_annotation.pl - now...
MODIFIED: ftp_download_ncbi_annotation.pl - fix...
MODIFIED: runPangenome.pl - corrected path to $...
MODIFIED: bin/make_BSR_trees.sh, bin/Newick-rub...
MODIFIED: run_iterative_pangenome.pl - switched...
ADDED: get_collection_date.pl - create a list o...
modified output of the index option
MODIFIED: run_iterative_pangenome.pl, runPangen...
MODIFIED: parse_genbank_files.pl - now attempts...
MODIFIED: run_iterative_pangenome.pl - now flus...
MODIFIED: runPangenome.pl, run_iterative_pangen...
reworded summary lines
added index option to pass fGIs index file to c...
MODIFIED: run_iterative_pangenome.pl - changed ...
MODIFIED: run_iterative_pangenome.pl - changed ...
MODIFIED: ftp_download_ncbi_annotation.pl - (1)...
MODIFIED: run_iterative_pangenome.pl - 1. optio...
MODIFIED: run_iterative_pangenome.pl - added --...
MODIFIED: check_att_files.pl - fixed bug encodi...
add ANI per cluster as last column of cluster_w...
MODIFIED: ftp_download_ncbi_annotation.pl - imp...
MODIFIED: check_att_files.pl - better descripti...
Fix lack of symmetry in blast matches affecting...
MODIFIED: runPangenome.pl - moves core_cluster_...
MODIFIED: runPangenome.pl - now uses blast+! A...
MODIFIED: run_iterative_pangenome.pl - changed ...
MODIFIED: run_iterative_pangenome.pl - minor ch...
fixing a graph repair problem in the bubble smo...
MODIFIED: pan_chromosome scripts have been upda...
MODIFIED: runPangenome.pl - more graphics scripts.
MODIFIED: ftp_download_ncbi_annotation.pl - now...
weight ANI/BSR distances by length of genes
track counts for inserts
MODIFIED: gene_order.pl, ftp_download_ncbi_anno...
MODIFIED: runPangenome.pl, pan_chromosome/graph...
ADDED: core_cluster_histogram.R
ADDED: pan_chromosome; MODIFIED: runPangenome.p...
MODIFIED: ftp_download_ncbi_annotation.pl - add...
MODIFIED: run_iterative_pangenome.pl - added --...
MODIFIED: ftp_download_ncbi_annotation.pl - tri...
MODIFIED: check_att_files.pl - now automaticall...
MODIFIED: ftp_download_ncbi_annotation.pl - new...
MODIFIED: run_iterative_pangenome.pl - now copi...
ADDED: check_att_files.pl - examine att_files t...
MODIFIED: ftp_download_ncbi_annotation.pl - now...
MODIFIED: run_iterative_pangenome.pl - centroid...
MODIFIED: run_iterative_pangenome.pl - now runs...
MODIFIED: ftp_download_ncbi_annotation.pl - add...
MODIFIED: ftp_download_ncbi_annotation.pl - new...
MODIFIED: ftp_download_ncbi_annotation.pl - cha...
MODIFIED: ftp_download_ncbi_annotation.pl - add...
MODIFIED: ftp_download_ncbi_annotation - now ac...
MODIFIED: download_ncbi_annotation.pl - revised...
MODIFIED: parse_genbank_files.pl - improved han...
MODIFIED: gene_order.pl - moved print_index cal...
MODIFIED: bin/ftp_download_ncbi_annotation.pl -...
MODIFIED: bin/ftp_download_ncbi_annotation.pl -...
MODIFIED: bin/ftp_download_ncbi_annotation.pl -...
MODIFIED: bin/ftp_download_ncbi_annotation.pl -...
MODIFIED: bin/ftp_download_ncbi_annotation.pl -...
MODIFIED: bin/ftp_download_ncbi_annotation.pl -...
MODIFIED: bin/ftp_download_ncbi_annotation.pl -...
MODIFIED: bin/ftp_download_ncbi_annotation.pl -...
MODIFIED: bin/ftp_download_ncbi_annotation.pl -...
ADDED: bin/ftp_download_ncbi_annotation.pl - In...
correcting bug in calculation of pairwise BSR c...
add R scripts for generating sample medoids as ...
change rules for setting pairwise BSR cutoffs t...
MODIFIED: bin/runPangenome.pl - revamped params...
make scripts more tolerant of different syntax
ADDED: lib/TIGR/FASTAgrammar.pm; MODIFIED: bin/...
MODIFIED: download_ncbi_annotation.pl - updated...
Tidy up options and add version
Add some versioning options and move readme out...
Home
Home
gene_order.pl added -L to usage and removed -L ...
MODIFIED: parse_genbank_file.pl, runPangenome.p...
update gene_order.pl with some minor bug fixes
Add starting from existing clusters, fix Jaccar...
MODIFIED: run_iterative_pangenome.pl - no longe...
MODIFIED: run_iterative_pangenome.pl - removed ...
changed fasta eutils to specify refseq, removin...
MODIFIED: runPangenome.pl - whitespace and inde...