Skip to content

Commit

Permalink
Update bug URL (bugzilla --> redmine)
Browse files Browse the repository at this point in the history
Thank you @lennax, noted on #47
  • Loading branch information
peterjc committed Apr 29, 2016
1 parent 4bd8c87 commit f0a0ad8
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion wiki/AlignIO.md
Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ The format name is a simple lowercase string, matching the names used in
|-------------------|-------|--------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| clustal | 1.46 | 1.46 | The [alignment format of Clustal X and Clustal W](http://bioperl.org/formats/alignment_formats/ClustalW_multiple_alignment_format.html "wikilink"). |
| emboss | 1.46 | No | The EMBOSS simple/pairs alignment format. |
| fasta | 1.46 | 1.48 | This refers to the *input* file format introduced for Bill Pearson's FASTA tool, where each record starts with a ">" line. Note that storing more than one alignment in this format is ambiguous. Writing FASTA files with AlignIO failed prior to release 1.48 (Bug [2557](http://bugzilla.open-bio.org/show_bug.cgi?id=2557)). |
| fasta | 1.46 | 1.48 | This refers to the *input* file format introduced for Bill Pearson's FASTA tool, where each record starts with a ">" line. Note that storing more than one alignment in this format is ambiguous. Writing FASTA files with AlignIO failed prior to release 1.48 (Bug [2557](https://redmine.open-bio.org/issues/2557)). |
| fasta-m10 | 1.46 | No | This refers to the pairwise alignment *output* from Bill Pearson's FASTA tools, specifically the machine readable version when the -m 10 command line option is used. The default free format text output from the FASTA tools is not supported. |
| ig | 1.47 | No | The refers to the IntelliGenetics file format often used for ordinary un-aligned sequences. The tool MASE also appears to use the same file format for alignments, hence its inclusion in this table. See [MASE format](http://bioperl.org/formats/alignment_formats/ClustalW_multiple_alignment_format.html "wikilink"). |
| maf | TBD | TBD | [Multiple Alignment Format (MAF)](Multiple_Alignment_Format "wikilink") produced by Multiz. Used to store whole-genome alignments, such as the 30-way alignments available from the UCSC genome browser. |
Expand Down

0 comments on commit f0a0ad8

Please sign in to comment.