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Table 6 Comparison of KnotAli with RNAalifold, Hxmatch, and Cacofold on two families with large variation in sequence length

From: KnotAli: informed energy minimization through the use of evolutionary information

family

Pre-shortened

Post-shortened

KnotAli

RNAalifold

Hxmatch

Cacofold

KnotAli

RNAalifold

Hxmatch

Cacofold

SRP-MAFFT

.415

.129

.134

.206

.582

.315

.300

.419

Group I intron-MAFFT

.396

.068

.069

.090

.547

.238

.339

.167

SRP-MUSCLE

.564

.241

.25

.255

.491

.198

.232

.200

Group I intron-MUSCLE

.461

.087

.064

.068

.463

.205

.138

.112

  1. Scores are compared between pre-shortened versions and post-shortened versions. Significance is shown between the algorithms on the pre-shortened and post-shortened results. For the significance of the post shortened results to the pre-shortened, see Additional file 3