From f0a0ad82446942506c7600304b0f37687161b99c Mon Sep 17 00:00:00 2001 From: peterjc Date: Fri, 29 Apr 2016 16:35:36 +0100 Subject: [PATCH] Update bug URL (bugzilla --> redmine) Thank you @lennax, noted on #47 --- wiki/AlignIO.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wiki/AlignIO.md b/wiki/AlignIO.md index e510e28b9..fff00f8a2 100644 --- a/wiki/AlignIO.md +++ b/wiki/AlignIO.md @@ -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. |