ClustAGE Activity
Brought to you by:
egonozer
Activity for ClustAGE
-
Egon A Ozer committed [ef6825]
Merge branch 'develop'
-
Added age set extension and ability to select external blast to use
-
added reference subelement capability
-
Merge branch 'develop'
-
ClustAGE released /ClustAGE_v0.8.linux.zip
-
-
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
1
