added a few more; to update later...

Author: lh3

_pages/software.md

@@ -8,7 +8,12 @@ permalink: /software
 
 ### Software
 
-#### Maintained by current members or functional with active users
+#### Developed by current members and functional
+
+* [Minimap2][sw-minimap2]: widely used long-read aligner,
+  published in [Li (2018)][pub-minimap2a] and [Li (2021)][pub-minimap2b].
+* [BWA][sw-bwa]: widely used short-read aligner,
+  published in [Li and Durbin (2009)][pub-bwa1], [Li and Durbin (2010)][pub-bwa2] and [Li (2013)][pub-bwa3].
 
 #### Developed by past members or maintained by others
 
@@ -17,13 +22,14 @@ permalink: /software
   Now part of the samtools project.
 * [Samtools][sw-samtools]: utilities for manipulating alignments in the SAM format.
   Initially published in [Li et al (2009)][pub-samtools1], [Li (2011a)][pub-samtools2] and [Li (2011b)][pub-samtools3].
-  Now maintained by Sanger since 2013.
+  Maintained by Sanger since 2013.
+* [TreeBeST][sw-treebest]: the core engine behind TreeFam for tree building.
+  Some components are described in [PI's thesis][pub-thesis].
+  Maintained by Ensembl Compara.
 
 ### Resources
 
-#### Published resources
-
-These resources have been updated since publication:
+#### Updated resources since publication
 
 * Ropebwt3 indices [for human][res-rb3-human] and [for bacteria][res-rb3-bac],
   initially published in [Li (2024)][pub-rb3].
@@ -41,7 +47,7 @@ These resources have been updated since publication:
 * [TreeFam][web-treefam]: database of animal gene trees.
   Published in [Li et al (2006)][pub-treefam1] and [Ruan et al (2008)][pub-treefam2],
   and described in [PI's thesis][pub-thesis].
-  No longer maintained.
+  No longer maintained since 2013.
 
 [res-rb3-human]: https://doi.org/10.5281/zenodo.13948741
 [res-rb3-bac]: https://doi.org/10.5281/zenodo.11533210
@@ -63,3 +69,11 @@ These resources have been updated since publication:
 [pub-treefam1]: https://pubmed.ncbi.nlm.nih.gov/16381935/
 [pub-treefam2]: https://pubmed.ncbi.nlm.nih.gov/18056084/
 [pub-thesis]: https://github.com/lh3/thesis
+[sw-treebest]: https://github.com/Ensembl/treebest
+[sw-minimap2]: https://github.com/lh3/minimap2
+[pub-minimap2a]: https://pubmed.ncbi.nlm.nih.gov/29750242/
+[pub-minimap2b]: https://pubmed.ncbi.nlm.nih.gov/34623391/
+[sw-bwa]: https://github.com/lh3/bwa
+[pub-bwa1]: https://pubmed.ncbi.nlm.nih.gov/19451168/
+[pub-bwa2]: https://pubmed.ncbi.nlm.nih.gov/20080505/
+[pub-bwa3]: https://arxiv.org/abs/1303.3997