Merge branch 'develop'
Added age set extension and ability to select external blast to use
added reference subelement capability
Merge branch 'develop'
updated readme
index AGE sequences in files instead of loading sequences to array
removed blastn multithreading. Fixed bug in sub-bin parsing.
changed subelement_to_tree matrix output to use NA instead of null for self-vs-self comparisons. Downstream R scripts like NA better.
memory and speed improvements in per-bin-position alignment handling
updated readme
removed File::Which dependency
updated README
added options for subelement border drawing and pdf output for graphics
Merge branch 'develop'
raw file format update. Option to turn off dust masking.
fixed bug in alignment file output and bug in splitting of sub-bins into sub-sub-bins. Also added unaligned AGE info to verbose output
several changes
made weighting by size default for Bray-Curtis calculations, added option to provide seed values instead of random
output formatting modifications and bug fix for subelement_annotation_stats.pl
added option to weight Bray-Curtis by subelement lengths to subelements_to_tree.pl
added clustage_read_confirm.pl to repository
readme fixes
readme fixes
fixed readme figures
minor changes to sublements_to_tree output files
remove leading or trailing spaces from genome IDs in subelement_csv_to_phylip.pl
added ability for subelements_to_tree.pl to collapse branches below minimum threshold bootstrap support
updated readme and license information
Updated README
fixed typo in re-rank.pl
added subelements_to_tree.pl to utilities
subelements_to_tree.pl now can search for needed phylip applications in PATH or in bin folder
updated re-rank.pl for new subelements.key.txt format. Also re-rank.pl now produces figures using gnuplot
started v0.7.5, filter read coverage data so only extending data included, clean up output formatting, remove redunant code
skip all-N bin representatives
sanity check on automatic thread population for non-Darwin platforms
added utility scripts for read count and annotation statistics
fixed bug that prevented some read corrections not to be output to key.txt or csv files
added per genome subelement distribution table ...
raw alignment data file output; sanity checking...
added option to use pre-determined reference AG...
Added output for gui frontend. Allow Excel line...
fixed bug preventing some read corrections from...
removed CGView XML output
added subelement sequence output
color gradients in graph output
added license
modifications to web output
alignments added by read correction displayed m...
fixed glitch where read correction was breaking...
deal with blank rank values
Added tkx GUI script
fixed a minor issue where segments that were ex...
few more output file header tweaks
Added output of read-corrected subelement seque...
limit bwa threads to 16 or less as memory alloc...
added subelement sequence size to log output
Fixed web output. Also fixed error in options i...
Add README and 3rd party copyright info
Minor web output fixes
gnuplot terminal automatically selected based o...
changed bin_end to bin_stop in output to better...
added binaries to git
web output tweaks
tweaked column headers on AGEs.annotations.txt ...
Add README and 3rd party copyright info
replaced arrow subroutine (accidentally removed...
binary file check
Added annotations to output figures
added minimum alignment length option
fixed annotation arrow head lengths
initial commit to git
added option for web-style output