TreeRefiner 1.1 – Refining Multiple Sequence Alignments

TreeRefiner 1.1

:: DESCRIPTION

TREEREEFINER is an efficient program for refining multiple alignment of genomic sequences based on a phylogenetic tree. It has demonstrated significant improvements in the accuracy of alignments generated by several popular aligners

::DEVELOPER

TreeRefiner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

TreeRefiner

:: MORE INFORMATION

Citation

Proc IEEE Comput Syst Bioinform Conf. 2005:111-9.
TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree.
Manohar A, Batzoglou S.

ProGraphMSA 20130709 – Fast and Robust Phylogeny-Aware Multiple Sequence Alignment

ProGraphMSA 20130706

:: DESCRIPTION

ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide tree.

::DEVELOPER

Adam M. Szalkowski

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
CMake
tclap
Eigen

:: DOWNLOAD

ProGraphMSA

:: MORE INFORMATION

Citaion

BMC Bioinformatics. 2012 Jun 13;13:129. doi: 10.1186/1471-2105-13-129.
Fast and robust multiple sequence alignment with phylogeny-aware gap placement.
Szalkowski AM.

RNAlign2D – Multiple Sequence Alignment of RNA using MUSCLE and Secondary Structure data

RNAlign2D

:: DESCRIPTION

RNAlign2D is a Python wrapper allowing one to align multiple RNA molecules using information about secondary structure and sequence. For this purpose MUSCLE program is used, but one can adjust it to use any other multiple sequence alignment tool.

::DEVELOPER

RNA Bioscience Initiative

:: REQUIREMENTS

Linux / MacOsX
Python
MUSCLE

:: DOWNLOAD

RNAlign2D

:: MORE INFORMATION

Citation

Woźniak T, Sajek M, Jaruzelska J, Sajek MP.
RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix.
BMC Bioinformatics. 2021 Oct 16;22(1):504. doi: 10.1186/s12859-021-04426-8. PMID: 34656080; PMCID: PMC8520625.

MSAVis – Multiple Sequence Alignment Visualization system

MSAVis

:: DESCRIPTION

MSAVis is a multiple sequence alignment visualization system that integrates the display of conserved domain data.

:: DEVELOPER

AgBase

:: SCREENSHOTS

:: REQUIREMENTS

Windows /Linux/MacOsX
Python
BioPython
wxPython
NumPy
PyOpenGL

:: DOWNLOAD

MSAVis

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S7. doi: 10.1186/1471-2105-10-S11-S7.
Exploratory visual analysis of conserved domains on multiple sequence alignments.
Jankun-Kelly TJ, Lindeman AD, Bridges SM.

Spial – Analysis of Subtype-specific Features in multiple Sequence Alignments of Proteins

Spial

:: DESCRIPTION

Spial (Specificity in alignments) is a web-server that takes a pair of multiple sequence alignments as input and produces an output that highlights positions which are conserved in both alignments (the consensus), and positions which are specific to either alignment.

::DEVELOPER

Spial team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Nov 15;26(22):2906-7. doi: 10.1093/bioinformatics/btq552. Epub 2010 Sep 29.
Spial: analysis of subtype-specific features in multiple sequence alignments of proteins.
Wuster A1, Venkatakrishnan AJ, Schertler GF, Babu MM.

RELINDEL 1.0 – Confidence Score for Indels in Multiple Sequence Alignment

RELINDEL 1.0

:: DESCRIPTION

RELINDEL (RELiable INDELs) is a method to quantify the reliability of indel characters by measuring how often they appear in a set of alternative multiple sequence alignments.

:: DEVELOPER

RELINDEL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

RELINDEL

:: MORE INFORMATION

Citation:

Indel reliability in indel-based phylogenetic inference.
Ashkenazy H, Cohen O, Pupko T, Huchon D.
Genome Biol Evol. 2014 Nov 18;6(12):3199-209. doi: 10.1093/gbe/evu252.

R3D-2-MSA – RNA 3D Structure-to-Multiple Sequence Alignment Server

R3D-2-MSA

:: DESCRIPTION

R3D-2-MSA enables users to select nucleotides from representative RNA 3D structures and seamlessly access sequence variants from large and diverse sequence alignments.

::DEVELOPER

Leontis-Zirbel Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Jun 5. pii: gkv543.
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.
Cannone JJ, Sweeney BA, Petrov AI, Gutell RR, Zirbel CL, Leontis N

PICS-Ord – Extract Phylogeny Information from hard-to-align Regions of Multiple Sequence Alignments

PICS-Ord

:: DESCRIPTION

PICS-Ord (Pairwise Identity and Cost Scores Ordination) is a method to extract phylogeny information from hard-to-align regions of multiple sequence alignments.

::DEVELOPER

The Cartwright Lab @ ASU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows
C ++ Compiler
Ngila

:: DOWNLOAD

PICS-Ord

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Jan 7;12:10. doi: 10.1186/1471-2105-12-10.
PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination.
Lücking R, Hodkinson BP, Stamatakis A, Cartwright RA.

BMGE 1.12 – Selection of Phylogenetic Informative Regions from Multiple Sequence Alignments

BMGE 1.12

:: DESCRIPTION

BMGE (Block Mapping and Gathering using Entropy) is a program that selects regions in a multiple sequence alignment that are suited for phylogenetic inference.

::DEVELOPER

BMGE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS