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Table 5 Performance of MCALIGN2 and AVID compared by estimator of divergence time based on a General Time-Reversible Model

From: MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution

Simulated

 

Alignment Estimated

t

Θ

Alignment Known

AVID

MCALIGN2(JC)

MCALIGN2(K2P)

MCALIGN2(GTR)

0.05

0.225

0.0504 (0.0100)

0.0523 (0.0181)

0.0501 (0.0100)

0.0500 (0.0100)

0.0500 (0.0100)

0.10

0.225

0.0991 (0.0145)

0.1023 (0.0159)

0.0981 (0.0151)

0.0976 (0.0149)

0.0983 (0.0149)

0.15

0.225

0.1522 (0.0191)

0.1575 (0.0226)

0.1496 (0.0192)

0.1494 (0.0192)

0.1502 (0.0194)

0.20

0.225

0.2034 (0.0225)

0.2131 (0.0283)

0.1985 (0.0238)

0.1978 (0.0239)

0.2003 (0.0235)

0.25

0.225

0.2531 (0.0286)

0.2699 (0.0383)

0.2493 (0.0316)

0.2453 (0.0308)

0.2491 (0.0311)

0.30

0.225

0.3003 (0.0302)

0.3222 (0.0420)

0.2944 (0.0324)

0.2914 (0.0311)

0.2987 (0.0323)

0.15

0.10

0.1520 (0.0207)

0.1528 (0.0219)

0.1510 (0.0203)

0.1508 (0.0203)

0.1510 (0.0204)

0.15

0.30

0.1509 (0.0200)

0.1634 (0.0301)

0.1489 (0.0207)

0.1470 (0.0208)

0.1499 (0.0207)

0.15

0.40

0.1526 (0.0208)

0.1794 (0.0398)

0.1507 (0.0213)

0.1477 (0.0203)

0.1508 (0.0211)

  1. Estimates of sequence divergence,t, from 200 replicates for each combination of t and θ, with sequences of Length 500 base pairs. Estimated root mean square error (e.r.m.s.e.) is shown after divergence time in parentheses. Here MCALIGN2 is tested by assuming either the correct model of DNA evolution(GTR) or the incorrect models (JC and K2P).