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Issues list

How to keep only one sequence per species (after the remonal of the outliers)?
#62 opened Jul 12, 2018 by yannisdim updated Jul 12, 2018
Auto-generate short methods section?
#59 opened Jun 22, 2015 by kcranston updated Jun 23, 2015
1
When pickle_pj, confirm pickle name == repo description
#58 opened May 29, 2015 by szitenberg updated May 29, 2015
Things to fix before publication
#56 opened Apr 21, 2015 by szitenberg updated May 14, 2015
Report scalability
#50 opened Jan 22, 2015 by szitenberg updated Apr 27, 2015
exonerate_ryo_to_gb
#55 opened Apr 20, 2015 by szitenberg updated Apr 20, 2015
Allow opting-out droping seq poor loci in alignment
#54 opened Apr 20, 2015 by szitenberg updated Apr 20, 2015
consider to_dict or index for pj.records. IMPORTANT bug
#43 opened Nov 26, 2014 by szitenberg updated Mar 9, 2015
1
TreSpex
#21 opened Oct 21, 2014 by szitenberg updated Jan 22, 2015
Genbank records without a sequence break the genbank parser bug
#30 opened Nov 4, 2014 by szitenberg updated Jan 22, 2015
Some needed checks for concatenations
#35 opened Nov 24, 2014 by szitenberg updated Jan 22, 2015
In pj.align, change the Conf objects list to a positional argument.
#42 opened Nov 26, 2014 by szitenberg updated Jan 22, 2015
possible biopython sequence statistics to add
#45 opened Dec 2, 2014 by szitenberg updated Jan 22, 2015
add raxmlHPC ­f S alignment column statistic?
#46 opened Dec 10, 2014 by szitenberg updated Jan 22, 2015
make 'iterate non source features'
#49 opened Dec 16, 2014 by szitenberg updated Jan 22, 2015
1
get list_loci_in_genbank to also accept embl files
#44 opened Nov 26, 2014 by szitenberg updated Nov 26, 2014
allow to modify the sequence header in project.write_by_locus()
#40 opened Nov 25, 2014 by szitenberg updated Nov 25, 2014
project.tree_summaries, project.trimming_summaries
#37 opened Nov 24, 2014 by szitenberg updated Nov 24, 2014
Make pdf version of the report enhancement
#23 opened Oct 22, 2014 by szitenberg updated Oct 22, 2014
@szitenberg
default node support annotaions enhancement
#14 opened Oct 17, 2014 by szitenberg updated Oct 17, 2014
Add thread to the MafftCommandLine calss enhancement
#13 opened Oct 17, 2014 by szitenberg updated Oct 17, 2014
@szitenberg
When filter_by_length, notify about depleted loci and kick them out bug
#11 opened Oct 17, 2014 by szitenberg updated Oct 17, 2014
@szitenberg
To Do: Add a list of trimmed position numbers to trim results enhancement
#9 opened Oct 16, 2014 by szitenberg updated Oct 16, 2014
@szitenberg
ToDo: make RpGit configurable enhancement
#5 opened Oct 16, 2014 by szitenberg updated Oct 16, 2014
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