# Help extracting pairwise alignments from MAFs **URL:** \ **Category:** usegalaxy.org support\ **Tags:** maf-manipulations\ **Created:** [March 2, 2021, 9:12am UTC](https://help.galaxyproject.org/t/help-extracting-pairwise-alignments-from-mafs/5481 "2021-03-02T09:12:06Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![jamesdgalbraith](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jamesdgalbraith/32/2194_2.png) [@jamesdgalbraith](https://help.galaxyproject.org/u/jamesdgalbraith)\ **Post date:** [March 2, 2021, 9:12am UTC](https://help.galaxyproject.org/t/help-extracting-pairwise-alignments-from-mafs/5481/1 "2021-03-02T09:12:06Z")
Hi, I’ve been attempting to extract the pairwise alignments from the human and zebrafish genomes using the “Extract Pairwise MAF Blocks” tool but had no success. A few years ago I was able complete this with hg19 and danRer5 and after reading another support ticket from Feb 2019 I assume hg19 is the assembly still indexed. Whenever I run the tool I am met with the error “The MAF source specified (PAIRWISE\_hg19\_danRer5) appears to be invalid”. I have attempted this with other assemblies and been met with the same error (eg human vs chimp and human vs mouse). Is there something I’m missing? Cheers, James. ---
**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\ **Post date:** [March 3, 2021, 3:56pm UTC](https://help.galaxyproject.org/t/help-extracting-pairwise-alignments-from-mafs/5481/2 "2021-03-03T15:56:27Z")
Hi @jamesdgalbraith, it seems to be a bug in the tool. The error has been reported [Error with Extract Pairwise MAF Blocks tool · Issue #3514 · galaxyproject/tools-iuc · GitHub](https://github.com/galaxyproject/tools-iuc/issues/3514). Regards ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [April 18, 2026, 12:21am UTC](https://help.galaxyproject.org/t/help-extracting-pairwise-alignments-from-mafs/5481/3 "2026-04-18T00:21:52Z")
2026 Update! Please see → [MAF manipulation tools in Galaxy: step by step publication with an example shared history](https://help.galaxyproject.org/t/10091/) ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [April 18, 2026, 12:21am UTC](https://help.galaxyproject.org/t/help-extracting-pairwise-alignments-from-mafs/5481/4 "2026-04-18T00:21:58Z")