Popular repositories
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horizontalTransfer
horizontalTransfer PublicCode used to infer and filter horizontal transfer events in eukaryotes. GPL Version 3 license.
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L1-dynamics
L1-dynamics PublicSample code to accompany the L1 evolutionary dynamics across eukaryotes manuscript. Shows how to perform two independent extraction methods: iterative search using LASTZ on genomic data, versus tra…
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regionalGenomeTurnover
regionalGenomeTurnover PublicScripts that were used in "Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse"
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Tuatara-paper
Tuatara-paper PublicContains the scripts used to analyse tuatara transposable elements, generate figures for tautara paper and infer phylogenies
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HTT_detection
HTT_detection PublicMethods for detection of horizontal transfer of transposable elements from genome sequences. GPL version 3 license.
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Elephant-project
Elephant-project PublicContains the scripts used to convert BAM to BED, generate binary sequences and infer phylogenies.
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Repositories
- HTT_detection Public
Methods for detection of horizontal transfer of transposable elements from genome sequences. GPL version 3 license.
- horizontalTransfer Public
Code used to infer and filter horizontal transfer events in eukaryotes. GPL Version 3 license.
- Tuatara-paper Public
Contains the scripts used to analyse tuatara transposable elements, generate figures for tautara paper and infer phylogenies
- regionalGenomeTurnover Public
Scripts that were used in "Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse"
- retrotransposonAccumulation Public
- Elephant-project Public
Contains the scripts used to convert BAM to BED, generate binary sequences and infer phylogenies.
- L1-dynamics Public
Sample code to accompany the L1 evolutionary dynamics across eukaryotes manuscript. Shows how to perform two independent extraction methods: iterative search using LASTZ on genomic data, versus translated nucleotide search of NCBI databases using TBLASTN. Subsequent analyses use programs such as MUSCLE, USEARCH, HMMER, etc.
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