Tag: Compatibility

clan_check v1.3 – Check Trees for compatibility with Defined Clans

clan_check v1.3

:: DESCRIPTION

Clan_Check analyses single-copy phylogenetic trees to assess if they violate clans defined by the user. This is designed for large-scale phylogenomic analyses where the user may have thousands of phylogenetic trees. This tool can help enrich the data for orthologs, by identifying where paralogy has caused violation of “well known” clans in outgroups.

::DEVELOPER

The Creevey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Clan_Check

:: MORE INFORMATION

Citation

Siu-Ting, Karen, et al.
Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics.
Molecular biology and evolution (2019).

BetaWrap / BetaWrapPro – Scores Sequences for Compatibility with the Right-handed beta-helix Fold

BetaWrap / BetaWrapPro

:: DESCRIPTION

BetaWrap is a program that scores sequences for compatibility with the right-handed beta-helix fold. It incorporates structural features of the known beta-helix structures, as well as residue pair preferences learned from beta-sheets in non-beta-helices, to generate and score potential wraps of a query sequence into a beta-helical structure. It computes a score and P-value which reflect how well a query sequence fits into the structural template, and returns the top-scoring parses of the sequence into multiple rungs.

The BetaWrapPro program predicts right-handed beta-helices and beta-trefoils by using both sequence profiles and pairwise beta-strand interactions, and returns coordinates for the structure.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BETAWRAP: successful prediction of parallel beta -helices from primary sequence reveals an association with many microbial pathogens.
Bradley P, Cowen L, Menke M, King J, Berger B.
Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):14819-24.

Proteins. 2006 Jun 1;63(4):976-85.
Fold recognition and accurate sequence-structure alignment of sequences directing beta-sheet proteins.
McDonnell AV, Menke M, Palmer N, King J, Cowen L, Berger B.

MultiPLX 2.1 – Analyze PCR Primer Compatibility

MultiPLX 2.1

:: DESCRIPTION

MultiPLX is a tool for analyzing PCR primer compatibility and automatically finding optimal multiplexing (grouping) solution. It uses state-of-the-art nearest neighbour DNA binding thermodynamics to estimate possible unwanted pairings between PCR samples.

MultiPLX Online Version

::DEVELOPER

Department of Bioinformatics, University of Tartu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 MultiPLX

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Apr 15;21(8):1701-2. Epub 2004 Dec 14.
MultiPLX: automatic grouping and evaluation of PCR primers.
Kaplinski L, Andreson R, Puurand T, Remm M.