CoMap 1.5.2 – Map Substitutions on a Phylogeny and Detect Coevolution

CoMap 1.5.2

:: DESCRIPTION

CoMap performs two kinds of tasks:

(Weighted) Probabilistic substitution mapping – Compute all (weighted) number of substitutions occurring on each branch of a tree, for each site of an alignment.
Co-evolution analysis – Using the substitution mapping, look for significantly groups of sites departing the null hypothesis of independence. Two kind of analyzes are provided: a pairwise analysis, presented in Dutheil et al. (2005), and a clustering analysis in Dutheil and Galtier (2007). In both cases, a parametric bootstrap approach is used to evaluate the significance of groups. Simulation results are written to separate files, a statistics software like R is required to look for the significance.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Bio++

:: DOWNLOAD

CoMap

:: MORE INFORMATION

Cite the following article if you use the pairwise method:

Dutheil J, Pupko T, Jean-Marie A, Galtier N.
A model-based approach for detecting coevolving positions in a molecule.
Mol Biol Evol. 2005 Sep;22(9):1919-28.

Cite the following article if you use the clustering method:

Dutheil J, Galtier N.
Detecting groups of co-evolving positions in a molecule: a clustering approach.
BMC Evol Biol. 2007 Nov 30;7(1):242

Cite the following article if you use the candidate approach method:

Dutheil JY, Jossinet F, Westhof E.
Base pairing constraints drive structural epistasis in ribosomal RNA sequences.
Mol Biol Evol. 2010 Aug;27(8):1868-76

GenGIS 2.5.3 – Combine Digital Map data with Genomic Data

GenGIS 2.5.3

:: DESCRIPTION

GenGIS is a bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GenGIS

:: MORE INFORMATION

Citation:

Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S and Beiko RG. 2009.
GenGIS: A geospatial information system for genomic data.
Genome Research, 19: 1896-1904

EM-SURFER – Navigating 3D Electron Microscopy Maps

EM-SURFER

:: DESCRIPTION

EM-SURFER is a web platform for real-time electron microscopy database search. It compares isosurface shape of a query EM map against maps in the latest EMDB.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Navigating 3D electron microscopy maps with EM-SURFER.
Esquivel-Rodríguez J, Xiong Y, Han X, Guang S, Christoffer C, Kihara D.
BMC Bioinformatics. 2015 May 30;16:181. doi: 10.1186/s12859-015-0580-6.

MAPanalyzer – Analyzing Microtubule-associated Proteins

MAPanalyzer

:: DESCRIPTION

MAPanalyzer is a MAP (Microtubule-associated Proteins) analysis tool.

::DEVELOPER

Ziding Zhang’s Lab, China Agricultural University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins.
Zhou Y, Yang S, Mao T, Zhang Z.
Database (Oxford). 2015 Nov 13;2015. pii: bav108. doi: 10.1093/database/bav108.

xMAN 20060925 – MAp OligoNucleotides to Subject Genome

xMAN 20060925

:: DESCRIPTION

xMAN (extreme MApping of OligoNucleotides) is a simple and efficient method for the mapping of millions of query oligonucleotide fragments to the subject genome of any given length. xMAN is at least an order of magnitude faster than other popular existing tools.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  xMAN

:: MORE INFORMATION

Citation:

Li W, Carroll JS, Brown M, Liu S.
xMAN: extreme MApping of OligoNucleotides.
BMC Genomics. 2008;9 Suppl 1:S20.

CREST 1.0.1 – uses the soft-clipped reads to directly Map the Breakpoints of SVs

CREST 1.0.1

:: DESCRIPTION

CREST (clipping reveals structure) is an algorithm that uses next-generation sequencing reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level of resolution.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  CREST

:: MORE INFORMATION

Citation

Jianmin Wang et al.
CREST maps somatic structural variation in cancer genomes with base-pair resolution
Nature Methods 8, 652–654 (2011)

NextGenMap 0.5.5 – Map NGS Reads against a Reference Genome

NextGenMap 0.5.5

:: DESCRIPTION

NextGenMap/NGM (Next Generation Mapper)is a computer program to map NGS reads against a reference genome using CPUs or GPUs.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NextGenMap

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 1;29(21):2790-1. doi: 10.1093/bioinformatics/btt468.
NextGenMap: fast and accurate read mapping in highly polymorphic genomes.
Sedlazeck FJ, Rescheneder P, von Haeseler A.

MAP 20121108 – A de novo Metagenomic Assembly program for Shotgun DNA reads

MAP 20121108

:: DESCRIPTION

MAP (Metagenomic Assembly program) is a de novo assembly approach and its implementation based on an improved Overlap/Layout/Consensus (OLC) strategy incorporated with several special algorithms.MAP uses the mate pair information, resulting in being more applicable to shotgun DNA reads (recommended as > 200 bp) currently widely-used in metagenome projects. Results of extensive tests on simulated data show that MAP can be superior to both Celera and Phrap for typical longer reads by Sanger sequencing, as well as has an evident advantage over Celera, Newbler, and the newest Genovo, for typical shorter reads by 454 sequencing.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MAP

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 1;28(11):1455-62. Epub 2012 Apr 11.
A de novo metagenomic assembly program for shotgun DNA reads.
Lai B, Ding R, Li Y, Duan L, Zhu H.

rMAPS 2.0.0 – RNA Map analysis and Plotting server for alternative Exon Regulation

rMAPS 2.0.0

:: DESCRIPTION

rMAPS (rna Map Analysis and Plotting Server) is a web server that systematically generates RNA-maps for the analysis of RNA-binding proteins (RBPs) binding sites which have position-dependent functions.

::DEVELOPER

rMAPS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

rMAPS: RNA map analysis and plotting server for alternative exon regulation.
Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y.
Nucleic Acids Res. 2016 May 12. pii: gkw410.

PLABQTL 20100816 – computer program to Map QTL

PLABQTL 20100816

:: DESCRIPTION

PLABQTL (PLAnt Breeding QTL analysis)is a program written for the detection of loci which affect the variation of quantitative traits. Its main purpose is to localize and characterize QTL (Quantitative
Trait Loci).

::DEVELOPER

H. Friedrich Utz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • windows

:: DOWNLOAD

PLABQTL

:: MORE INFORMATION

Citation

Utz and Melchinger, 1996:
PLABQTL: A program for composite interval mapping of QTL.
Journal of Agricultural Genomics 2, 1-5