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Commits on Feb 16, 2014

• Python 3 fix for MUSCLE subprocess example, issue biopython#284

  peterjc

  committed
  522a693

Commits on Feb 14, 2014

• Entrez DTD http://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060131/esummary-v1.dtd

  Show description for cb560e7
  peterjc

  committed
  cb560e7

Commits on Feb 13, 2014

• Adding http://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060628/esearch.dtd

  Show description for 6c2e7db
  peterjc

  committed
  6c2e7db

• Update for TogoWS convert - don't use urlencode & data= prefix anymore

  peterjc

  committed
  772a24c

Commits on Feb 9, 2014

• Document concatenating Seq objects with sum in Tutorial

  Show description for 43d3ef3
  peterjc

  committed
  43d3ef3

Commits on Feb 6, 2014

• Install BWA under TravisCI to test the wrapper

  peterjc

  committed
  c0431b1

• Comment out unimplemented test functions

  Show description for a8ff1e0
  peterjc

  committed
  a8ff1e0

• Removed print statements; Use assertEqual

  peterjc

  committed
  582c321

• Windows case insensitive; Actually use the detected bwa binary

  peterjc

  committed
  ff9db70

• Windows case insensitive; Actually use the detected samtools binary

  peterjc

  committed
  7c9e442

Commits on Feb 5, 2014

• Install samtools under TravisCI (to test wrapper)

  peterjc

  committed
  e0bde31

• Thank Saket for the samtools wrapper

  peterjc

  committed
  30256af

• Adding wrapper for the samtools command line tool

  Show description for 768622a
  peterjc

  committed
  768622a

• Formatting changes

  

  saketkc

  authored and

  peterjc

  committed
  82f03af

• Class docstring; fix typo; use comment not multiline string

  peterjc

  committed
  d6156fc

• Adding _AurgumentList for passing in multiple filenames for the samtools wrapper

  Show description for 019796c
  

  saketkc

  authored and

  peterjc

  committed
  019796c

• Talk about strict vs relaxed PHYLIP; Fixed extra bracket

  peterjc

  committed
  749de04

Commits on Feb 1, 2014

• AlignIO chapter didn't talk about relaxed PHYLIP support

  peterjc

  committed
  55e1ffd

Commits on Jan 30, 2014

• Update Scanner.py

  

  azalea

  authored and

  peterjc

  committed
  29d490b

• Changed a typo in comment

  

  azalea

  authored and

  peterjc

  committed
  942e98b

Commits on Jan 29, 2014

• Thank Edward Liaw for Python 3 Bio.Entrez fix

  peterjc

  committed
  2f6c288

• Add test for elink, esearch, and webenv

  edliaw

  committed
  85b9abd

Commits on Jan 28, 2014

• Iterate through copy of dictionary when deleting None values

  edliaw

  committed
  dc2208d

• majority_consensus: ensure stable ordering so output tree is always the same.

  Show description for f44df7d
  etal

  committed
  f44df7d

• Consensus: extracted repeated code into _BitString.from_bool, _clade_to_bitstr,

  Show description for cc2b363
  etal

  committed
  cc2b363

Commits on Jan 27, 2014

• Jython's XML tags are in the other order

  peterjc

  committed
  b31bbfe

• Update expected test output for SwissProt to SeqXML

  peterjc

  committed
  a55023e

• Ignore empty list of taxon ids in SeqXML writer

  peterjc

  committed
  ac1ea71

Commits on Jan 26, 2014

• Test species preservation on SwissProt to SeqXML conversion

  peterjc

  committed
  91810c8

• Another error in SeqXML reported by Alan Wilter

  Show description for d06e85d
  peterjc

  committed
  d06e85d

• Discrepancy in SwissProt parser and SeqXML regarding NCBI taxid

  peterjc

  committed
  50f47b8

Commits on Jan 23, 2014

• Fix variable name typo reported by Alan Wilter by email

  Show description for 0e23daf
  peterjc

  committed
  0e23daf

Commits on Jan 19, 2014

• Genepop Large File Parser bug

  tiagoantao

  committed
  f7f33ed

Commits on Jan 16, 2014

• Update doctest, deltablast does not have -ungapped

  peterjc

  committed
  a033ecc

• deltablast does not have -task, -ungapped, -db_hard_mask, -db_soft_mask

  Show description for 1f0c956
  peterjc

  committed
  1f0c956

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