QPALMA 0.9.3 – Optimal Spliced Alignments of Short Sequence Reads

QPALMA 0.9.3

:: DESCRIPTION

QPALMA is a software for computing accurate spliced alignments which takes advantage of the read’s quality information as well as computational splice site predictions. Our method uses a training set of spliced reads with quality information and known alignments. It uses a large margin approach similar to support vector machines to estimate its parameters to maximize alignment accuracy.

::DEVELOPER

Rätsch Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Python

:: DOWNLOAD

 QPALMA

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Aug 15;24(16):i174-80.
Optimal spliced alignments of short sequence reads.
De Bona F, Ossowski S, Schneeberger K, Rätsch G.

HHalign-Kbest 20150722 – Exploring Sub-optimal Alignments for remote Homology Comparative Modeling

HHalign-Kbest 20150722

:: DESCRIPTION

HHalign-Kbest is useful to automatically obtain optimized alignments and models in case of low sequence identity (<35%) between a query and a template protein. It can generate k suboptimal (e.g. top-k scoring) alignments rather than only the optimal one which may contain small to large errors.

::DEVELOPER

HHalign-Kbest team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

HHalign-Kbest

:: MORE INFORMATION

Citation

Yu J, Picord G, Tufféry P, Guerois R.
HHalign.KBest: exploring sub-optimal alignments for remote homology comparative modeling
Bioinformatics. 2015 Jul 30. pii: btv441.

DACTAL – Divide-and-Conquer Trees Without ALignments

DACTAL

:: DESCRIPTION

DACTAL is a software package for estimating phylogenies from ultra-large datasets with up to tens of thousands of unaligned nucleotide sequences and with many kb of sequence length.

::DEVELOPER

The Warnow Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/MacOsX
  • Python

:: DOWNLOAD

 DACTAL

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Jun 15;28(12):i274-82. doi: 10.1093/bioinformatics/bts218.
DACTAL: divide-and-conquer trees (almost) without alignments.
Nelesen S1, Liu K, Wang LS, Linder CR, Warnow T.

INSEGT 1.0 – Analyse Alignments of RNA-Seq reads using Gene Annotations

INSEGT 1.0

:: DESCRIPTION

INSEGT is a tool to analyse alignments of RNA-Seq reads (single-end or paired-end) by using gene annotations. It can measure exon, transcript and gene expression levels of given annotations. If read alignments span more than one exon, INSEGT can also compute possible exon combinations (tuple) and their expression levels. According to requirements it computes maximal tuple or tuple with a certain length. For paired-end reads INSEGT builds also tuple, whose exons are connected by matepairs. Briefly it searches the intervals of the read alignments in the intervals of the given annotations. It counts the mapped reads for each annotation and its parent annotation and stores the mapped annotations for each read.

::DEVELOPER

David Weese , Sabrina Krakau.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 INSEGT

:: MORE INFORMATION

COMPASS 3.1 – COmparison of Multiple Protein Sequence Alignments with assessment of Statistical Significance.

COMPASS 3.1

:: DESCRIPTION

COMPASS runs a search with submitted alignment (or sequence) as a query against a database of protein families.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 COMPASS

:: MORE INFORMATION

Citation:

R.I. Sadreyev, M. Tang, B. Kim and N.V. Grishin (2009)
COMPASS server for homology detection: improved statistical accuracy, speed, and functionality.
Nucleic Acids Res doi:10.1093/nar/gkp360.