LinAliFold and CentroidLinAliFold is fast MFE and MEA-based consensus secondary structure prediction software from RNA alignments using beam search, respectively.
Both tools can take the multi-FASTA format as an input file format, and predict its common secondary structure.
An example:
$ ./bin/LinAliFold -i sample.fasta
score:-23.13
(((((((..((((...........)))).(((((.......)))))...................(((((.......))))))))))))....
LinAliFold Options:
(Required)
-i STR InputFileName
(Optional)
-b INT The beam size [default:100]
-d INT The value of the parameter delta [default: 1.0]
-e INT The value of the parameter beta [default: 1.0]
-r INT Designation of the covariation score model 0: simple score model, 1: ribosum score model [defualt:0]
CentroidLinAliFold Options:
(Required)
-i STR InputFileName
(Optional)
-b INT The beam size [default:100]
-d INT The value of the parameter delta [default: 1.0]
-e INT The value of the parameter beta [default: 1.0]
-r INT Designation of the covariation score model 0: simple score model, 1: ribosum score model [defualt:0]
-g INT The value of the parameter gamma [default: 1.0]
-t DBL The threshold value for base pairing probabilities [default: 0.0001]
-w DBL The value of the mixture weight parameter [default: 0.5]
-p INT Designation of the selection method of gamma 0: user-defined parameter 1: maximization of the pseudo-expected accuracy of MCC [default: 0]
-o INT Designation of the output style 0: the bpp is not outputted 1: the bpp is outputted [default: 0]
For the meaning of parameters delta and beta, please see the following RNAaliFold paper [1].
[1] Bernhart, S.H., Hofacker, I.L., Will, S. et al. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 9, 474 (2008)
Version 1.0.0 (2022/06/17)
In developing this program, we referred to the source code from the LinearFold and LinearPartition. We thank Dr. Liang Huang and LinearFold development group. You can download the source code of LinearFold and LinearPartition from https://github.com/LinearFold/LinearFold and https://github.com/LinearFold/LinearPartition.
This software is released under the MIT License, see LICENSE.txt.
Tsukasa Fukunaga and Michiaki Hamada. "LinAliFold and CentroidLinAliFold: Fast RNA consensus secondary structure prediction for aligned sequences using beam search methods." under submission.