Stemloc-AMA specifications


Unique identifier OMICS_03742
Name Stemloc-AMA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for Stemloc-AMA

Stemloc-AMA citations


PicXAA R: Efficient structural alignment of multiple RNA sequences using a greedy approach

BMC Bioinformatics
PMCID: 3044294
PMID: 21342569
DOI: 10.1186/1471-2105-12-S1-S38

[…] of structural information. We picked these methods as they are among the fastest structural RNA aligners which yield high accuracy. There exists several other aligners such as RAF 1.00 [], Murlet [], Stemloc-AMA [], LARA 1.3.2 [], M-LocARNA [], and R-Coffee [], which have much higher complexity than MAFFT-xinsi (in some cases they are near 60 times slower) while their accuracy is usually worse or […]


Evolutionary Triplet Models of Structured RNA

PLoS Comput Biol
PMCID: 2725318
PMID: 19714212
DOI: 10.1371/journal.pcbi.1000483

[…] cestral structure, given phylogeny, descendant structures and correct model); Stemloc (a greedy ML heuristic, ignoring phylogeny in favor of a single-linkage clustering of the descendant structures); Stemloc-AMA (a posterior-decoding heuristic, maximizing the alignment's expected accuracy rather than its likelihood); and Handel (ML alignment under various indel models that ignore secondary structu […]

Stemloc-AMA institution(s)
Biophysics Graduate Group, Department of Mathematics and Department of Bioengineering, University of California, Berkeley, CA, USA

Stemloc-AMA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Stemloc-AMA