Tag: Lineage

LIGAP 20130505 – Identify Condition/Lineage Specific Time-course Profiles

LIGAP 20130505

:: DESCRIPTION

LIGAP allows integrative analysis and visualization of multiple lineages over whole time-course profiles.

::DEVELOPER

Computational systems biology group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 LIGAP

:: MORE INFORMATION

Citation

BMC Genomics. 2012 Oct 30;13:572. doi: 10.1186/1471-2164-13-572.
An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation.
Aijö T, Edelman SM, Lönnberg T, Larjo A, Kallionpää H, Tuomela S, Engström E, Lahesmaa R, Lähdesmäki H.

linACC 0.1.4 – Detection of Lineage Specific Accelerated Substitution Rates

linACC 0.1.4

:: DESCRIPTION

linACC exploits a hierarchy of nested evolutionary models to detect lineage specific acceleraton of substitution rates in different species/branches.

::DEVELOPER

Kostka Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R

:: DOWNLOAD

linACC

:: MORE INFORMATION

Citation

Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages.
D Kostka, AK Holloway, KS Pollard
Molecular Biology and Evolution, 35(8):2034-2045 2018.

Clean_tree 2 – High-resolution Male Lineage Classification

Clean_tree 2

:: DESCRIPTION

Clean tree is a tool intended to help interpret phylogenetic SNP genotypes obtained from NGS-data, furthermore it uses a quality control system to ensure the accuracy of the obtained results.

::DEVELOPER

Dept Genetic Identification ErasmusMC Rotterdam

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R

:: DOWNLOAD

  Clean tree

:: MORE INFORMATION

Citation

Ralf, A., van Oven, M., Zhong, K., Kayser, M.
Simultaneous analysis of hundreds of Y-chromosomal SNPs for high-resolution paternal lineage classification using targeted semiconductor sequencing.
Hum Mutat. 2015 36: 151-9. PubMed: 25338970

Forensic Y-SNP analysis beyond SNaPshot: High-resolution Y-chromosomal haplogrouping from low quality and quantity DNA using Ion AmpliSeq and targeted massively parallel sequencing.
Ralf A, Oven M, Montiel González D, de Knijff P, van der Beek K, Wootton S, Lagacé R, Kayser M.
Forensic Science International: Genetics , 2019