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@agudys agudys released this 18 May 10:26
· 28 commits to master since this release
v2.0.0
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Learn about vigilant mode.

The following important changes have been introduced:

  • Fast guide tree heuristic called Medoid Tree (-medoidtree switch) for ultra-scale alignments:
    • the entire Pfam-A v33.1 in its largest NCBI variant (over 18 thousand families, 60 GB of raw FASTA files) was analyzed in 8 hours,
    • the famility PF00005 of 3 million ABC transporters was aligned in 5 minutes and 24 GB of RAM.
  • Remarkable time and memory optimizations - SLINK has been replaced with Prim’s minimum spanning tree algorithm when constructing default (single linkage) guide trees. NOTE: This may change quality results slightly compared to FAMSA 1 due to different ties resolution.
  • Neighbour joining guide trees (-gt nj option). NOTE: Neighbour joining trees are calculated with a use of original O(N3) algorithm, thus their applicability on large sets is limited (unless they are used as subtrees with Medoid Tree heuristic),
  • Option for compressing output aligment to gzip (-gz switch).
  • Compatibility with ARM64 8 architecture (including Apple M1).
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