Multiple genome alignment in the telomere-to-telomere assembly era

Table 2 Multiple genome alignment methods. Tools which only perform part of MGA or are only suited for pairwise genome alignment are excluded. Progressive aligners are italicized. See [24] for a comprehensive list of tools for all subproblems of MGA

Method	Anchor type	Anchor discovery method	Anchor chaining	MSA method
A-Bruijn Aligner [76]	Pairwise alignments	BlastZ [77]	Maximum Subgraph with Large Girth problem [78]	-
Cactus [79]	Pairwise alignments	LastZ [80] and BAR	Cactus alignment filter	Pecan [81]
M-GCAT [82]	MUMs	Compressed suffix graph	Recursive match chaining	MUSCLE [44]
Mauve [36]	MUMs	GRIL [83]	Greedily removes low-scoring LCBs	ClustalW [84]
MAVID [85, 86]	Exon Matches	BLAT [87] and GENSCAN [88]	Smith-Waterman [89]	Needleman-Wunsch [90]
Mugsy [91]	Pairwise alignments	MUMmer [92]	Min-Cut in alignment graph	T-Coffee [93]
Multi-Lagan [94]	Multiple short inexact words	CHAOS [95]	Longest increasing subsequence	Sum-of-pairs/consensus hybrid approach similar to ClustalW
Multiple Genome Aligner [96]	MEMs	Suffix array	Maximum-weight path in an acyclic graph [97]	ClustalW [84]
Parsnp [37]	MUMs	Compressed suffix graph	Weighted recursive match chaining	libMUSCLE [44]
Progressive Cactus [72]	Pairwise alignments	LastZ [80] and BAR	Cactus alignment filter	Pecan [81]
progressiveMauve [98]	Extending palindromic spaced seeds	ProcrastAligner [73]	Sum-of-pairs score	libMUSCLE [44]
SibeliaZ [99]	k-mers	TwoPaCo [100]	Carrying paths	SIMD partial order alignment [101]
SuperMap [102]	Multiple short inexact words	CHAOS [95]	Maximum Weight Path Cover	Progressive LAGAN [94]
TBA/MultiZ [41]	Pairwise alignments	BlastZ [77]	-	MultiZ [41]

ISSN: 1474-760X