v2.0.0-rc
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).