Jekyll2026-08-13T16:56:50+00:00https://www.arenaria.ca/feed.xmlGlenn Hickeypersonal description{"avatar"=>"arenaria.png", "name"=>nil, "pronouns"=>nil, "bio"=>"Arenaria Software Consulting Inc.", "location"=>"Canada", "employer"=>nil, "uri"=>nil, "email"=>"glenn.hickey@arenaria.ca", "bioarxiv"=>"https://www.biorxiv.org/search/author1%3AGlenn%2BHickey%2B", "googlescholar"=>"https://scholar.google.ca/citations?user=YM0669QAAAAJ", "impactstory"=>nil, "orcid"=>"https://orcid.org/0000-0002-2280-9404", "semantic"=>nil, "pubmed"=>"https://pubmed.ncbi.nlm.nih.gov/?term=Glenn+Hickey", "researchgate"=>nil, "scopus"=>nil, "bitbucket"=>nil, "codepen"=>nil, "dribbble"=>nil, "github"=>"glennhickey", "kaggle"=>nil, "stackoverflow"=>nil, "bluesky"=>nil, "facebook"=>nil, "flickr"=>nil, "foursquare"=>nil, "goodreads"=>nil, "google_plus"=>nil, "keybase"=>nil, "instagram"=>nil, "lastfm"=>nil, "linkedin"=>nil, "mastodon"=>nil, "medium"=>nil, "pinterest"=>nil, "soundcloud"=>nil, "steam"=>nil, "telegram"=>nil, "tumblr"=>nil, "twitter"=>nil, "vine"=>nil, "weibo"=>nil, "wikipedia"=>nil, "xing"=>nil, "youtube"=>nil, "zhihu"=>nil}glenn.hickey@arenaria.caUpdated 447-way Zoonomia Alignment2025-11-10T00:00:00+00:002025-11-10T00:00:00+00:00https://www.arenaria.ca/posts/2025/11/blog-post-1(I’m going to start posting notes on new alignments I’ve released, and maybe other related stuff, here….)

Zoonomia With Expanded Primates MAF (Take 3)

Sometimes it seems like converting a genome alignment from HAL to MAF is as difficult making the alignment in the first place. And despite recent progress on this subject (see cactus-hal2maf), an astute user (Irwin Jungreis) found several issues with the previous version of the MAFs posted for the 447-way Zoonomia alignment. Some of these issues had already been fixed in the tools but one, involving rows being incorrectly joined during normalization, persisted. Thanks to Irwin’s help, we finally fixed it, and the corrected alignment, generated with Cactus v3.0.1, can be found here.

]]>{"avatar"=>"arenaria.png", "name"=>nil, "pronouns"=>nil, "bio"=>"Arenaria Software Consulting Inc.", "location"=>"Canada", "employer"=>nil, "uri"=>nil, "email"=>"glenn.hickey@arenaria.ca", "bioarxiv"=>"https://www.biorxiv.org/search/author1%3AGlenn%2BHickey%2B", "googlescholar"=>"https://scholar.google.ca/citations?user=YM0669QAAAAJ", "impactstory"=>nil, "orcid"=>"https://orcid.org/0000-0002-2280-9404", "semantic"=>nil, "pubmed"=>"https://pubmed.ncbi.nlm.nih.gov/?term=Glenn+Hickey", "researchgate"=>nil, "scopus"=>nil, "bitbucket"=>nil, "codepen"=>nil, "dribbble"=>nil, "github"=>"glennhickey", "kaggle"=>nil, "stackoverflow"=>nil, "bluesky"=>nil, "facebook"=>nil, "flickr"=>nil, "foursquare"=>nil, "goodreads"=>nil, "google_plus"=>nil, "keybase"=>nil, "instagram"=>nil, "lastfm"=>nil, "linkedin"=>nil, "mastodon"=>nil, "medium"=>nil, "pinterest"=>nil, "soundcloud"=>nil, "steam"=>nil, "telegram"=>nil, "tumblr"=>nil, "twitter"=>nil, "vine"=>nil, "weibo"=>nil, "wikipedia"=>nil, "xing"=>nil, "youtube"=>nil, "zhihu"=>nil}glenn.hickey@arenaria.ca