TwinCons – Alignment Score for detection of Ancient Homologies

TwinCons

:: DESCRIPTION

TwinCons is a software to detect noisy signals of deep ancestry of proteins or nucleic acids.

::DEVELOPER

The Williams Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

TwinCons

:: MORE INFORMATION

Citation

Penev PI, Alvarez-Carreño C, Smith E, Petrov AS, Williams LD.
TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
PLoS Comput Biol. 2021 Oct 29;17(10):e1009541. doi: 10.1371/journal.pcbi.1009541. PMID: 34714829; PMCID: PMC8580257.

LeeHom 1.2.15 – Bayesian Reconstruction of Ancient DNA Fragments

LeeHom 1.2.15

:: DESCRIPTION

leeHom is a program for the Bayesian reconstruction of ancient DNA.

::DEVELOPER

Department of Genetics / Bioinformatics Group, Max Planck Institute for Evolutionary Anthropology, Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 LeeHom

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Feb 1;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.
leeHom: adaptor trimming and merging for Illumina sequencing reads.
Renaud G, Stenzel U, Kelso J

PALEOMIX 1.3.2 – Characterization of Ancient and Modern Genomes by SNP Detection and Phylogenomic and Metagenomic analysis

PALEOMIX 1.3.2

:: DESCRIPTION

The PALEOMIX pipeline is a user-friendly package designed for Unix-like systems and largely automates the analyses related to whole genome re-sequencing. It is compatible with a full range of sequence data and performs a series of user-defined analyses, including read trimming, collapsing of overlapping mate-pairs, read mapping, PCR duplicate removal, SNP calling, and metagenomic profiling.

::DEVELOPER

The Centre for Anthropobiology and Genomics of Toulouse

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PALEOMIX

:: MORE INFORMATION

Citation

Nat Protoc. 2014 May;9(5):1056-82. doi: 10.1038/nprot.2014.063. Epub 2014 Apr 10.
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.
Schubert M1, Ermini L1, Der Sarkissian C1, Jónsson H1, Ginolhac A1, Schaefer R2, Martin MD1, Fernández R1, Kircher M3, McCue M4, Willerslev E1, Orlando L1.

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