NimbleTree 2.6 – Make Phylogenetic Trees from Sequence Data

NimbleTree 2.6

:: DESCRIPTION

NimbleTree is a relatively user-friendly Windows program for making phylogenetic trees starting from sequence data.

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

NimbleTree

:: MORE INFORMATION

Before you download software you need to read disclaimer.

Genome Workbench 3.7.1 – View & Analyze Sequence Data

Genome Workbench 3.7.1

:: DESCRIPTION

Gbench (NCBI Genome Workbench) is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.

::DEVELOPER

Genome Workbench Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

Genome Workbench

:: MORE INFORMATION

ASAP 1.1.7 – Automated Sequence data Processing on Computer Clusters

ASAP 1.1.7

:: DESCRIPTION

ASAP (Advanced Sequence Automated Pipeline)is an open source pipeline designed to assist users in managing various jobs associated with processing HiSeq data on a cluster or in serial. . The software was designed to alleviate these issues by providing a modular system to allow users with different needs to process their data with a minimal amount of effort. In addition to minimizing human involvement, ASAP is designed to work on the researcher’s local computer cluster, if one is available

::DEVELOPER

Chun Li

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ASAP

:: MORE INFORMATION

Citation

BMC Res Notes. 2013 Jan 4;6:5. doi: 10.1186/1756-0500-6-5.
ASAP: an environment for automated preprocessing of sequencing data.
Torstenson ES1, Li B, Li C.

SEQMINER 8.0 – Efficiently Read Sequence Data into R

SEQMINER 8.0

:: DESCRIPTION

SEQMINER is an R package for annotating and querying files of sequence variants (e.g., VCF/BCF files) and summary association statistics (e.g., METAL/RAREMETAL files), and for integrating bioinformatics databases.

::DEVELOPER

SEQMINER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 SEQMINER

:: MORE INFORMATION

Citation

SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations.
Zhan X, Liu DJ.
Genet Epidemiol. 2015 Sep 23. doi: 10.1002/gepi.21918.

SpliceSeq 2.1 – Investigate alternative mRNA Splicing in Next Generation mRNA Sequence data

SpliceSeq 2.1

:: DESCRIPTION

SpliceSeq provides a quick, easy method of investigating alternative mRNA splicing in next generation mRNA sequence data. The tool may be used on a single mRNA-Seq sample to identify genes with multiple spliceforms or on a pair of samples to identify differential splicing between the samples. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 SpliceSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):2385-7. Epub 2012 Jul 20.
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.
Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN.

ClonalFrame 1.2 / ClonalFrameML 1.12 – Inference of Bacterial Microevolution using Multilocus Sequence data

ClonalFrame 1.2 / ClonalFrameML 1.12

:: DESCRIPTION

ClonalFrame is a computer package for the inference of bacterial microevolution using multilocus sequence data.In a nutshell, ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.ClonalFrame can be applied to any kind of sequence data, from a single fragment of DNA to whole genomes. It is well suited for the analysis of MLST data, where 7 gene fragments have been sequenced, but becomes progressively more powerful as the sequenced regions increase in length and number up to whole genomes. However, it requires the sequences to be aligned. If you have genomic data that is not aligned, we recommend using Mauve which produces alignment of whole bacterial genomes in exactly the format required for analysis with ClonalFrame.

ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes.

::DEVELOPER

Xavier Didelot and Daniel Wilson

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 ClonalFrame , ClonalFrameML

:: MORE INFORMATION

Citation

ClonalFrameML: efficient inference of recombination in whole bacterial genomes.
Didelot X, Wilson DJ.
PLoS Comput Biol. 2015 Feb 12;11(2):e1004041. doi: 10.1371/journal.pcbi.1004041.

Didelot and Falush (2007)
Inference of Bacterial Microevolution Using Multilocus Sequence Data
Genetics March 2007 vol. 175 no. 3 1251-1266

TrioCaller 20120626 / FamLDCaller 20160215 – LD-aware Genotype Calling and Phasing program for Sequence data

TrioCaller 20120626 / FamLDCaller 20160215

:: DESCRIPTION

TrioCaller is based on a LD-aware method to infer genotypes and phasing for sequencing in trios (or mixed with undrelated individuals).

FamLDCaller is an extension of TrioCaller to handle nuclear and general family structure.

::DEVELOPER

Abecasis Group / Chen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TrioCaller  / FamLDCaller

:: MORE INFORMATION

Citation

A computational method for genotype calling in family-based sequencing data.
Chang LC, Li B, Fang Z, Vrieze S, McGue M, Iacono WG, Tseng GC, Chen W.
BMC Bioinformatics. 2016 Jan 16;17(1):37. doi: 10.1186/s12859-016-0880-5.

Genome Res. 2013 Jan;23(1):142-51. doi: 10.1101/gr.142455.112. Epub 2012 Oct 11.
Genotype calling and haplotyping in parent-offspring trios.
Chen W1, Li B, Zeng Z, Sanna S, Sidore C, Busonero F, Kang HM, Li Y, Abecasis GR.

SequenceServer 2.0.0.rc8 – Set up a Local BLAST Web Server to Search & Share Sequence data

SequenceServer 2.0.0.rc8

:: DESCRIPTION

SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.

::DEVELOPER

Wurm Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SequenceServer

:: MORE INFORMATION

Citation

Sequenceserver: a modern graphical user interface for custom BLAST databases
Anurag Priyam, Ben J Woodcroft, Vivek Rai, Alekhya Munagala, Ismail Moghul, Filip Ter, Mark Anthony Gibbins, HongKee Moon, Guy Leonard, Wolfgang Rumpf, Yannick Wurm
doi: http://dx.doi.org/10.1101/033142

SeqToolBox 0.02 – A set of Perl modules and scripts for Operations on Sequence data

SeqToolBox 0.02

:: DESCRIPTION

SeqToolBox is a set of Perl modules and scripts for day to day operations on sequence data. Includes, parsers for standard file formats and some utility modules, such as modules for working with “sets”, a set of modules for handling NCBI taxonomy database etc. The bin directory contains some scripts to run jobs on clusters.

::DEVELOPER

Malay K Basu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  SeqToolBox

:: MORE INFORMATION

RADAR v0.2.4 – Differential Methylation analysis for m6A Sequence data

RADAR v0.2.4

:: DESCRIPTION

RADAR is a comprehensive analytical tool for detecting differentially methylated loci in MeRIP-seq data.

::DEVELOPER

Chen Group at U Chicago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX

:: DOWNLOAD

RADAR

:: MORE INFORMATION

Citation

Zhang Z, Zhan Q, Eckert M, Zhu A, Chryplewicz A, De Jesus DF, Ren D, Kulkarni RN, Lengyel E, He C, Chen M.
RADAR: differential analysis of MeRIP-seq data with a random effect model.
Genome Biol. 2019 Dec 23;20(1):294. doi: 10.1186/s13059-019-1915-9. PMID: 31870409; PMCID: PMC6927177.