🌲👻 Testing the phylogenetic reality of the living fossil with an EDBMM
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Updated
Jan 7, 2017 - R
🌲👻 Testing the phylogenetic reality of the living fossil with an EDBMM
This was a project performed by Charles Sansone with assistance from Dr. Lauren Sallan over Summer 2017. Using data science packages in R along with other programs like Mesquite and MrBayes, extrapolated the likely starting water environment of ancient extinct fish
MrBayes optimized with AVX512 and FMA
EMnEM is a DNA motif finder that takes multiple alignments and a phylogenetic tree and identifies conserved patterns
Phylogeny and species trait effects on detectability
Perl libraries for handling rRNA annotated multiple sequence alignments, and more
Udo Stenzel's perl-ngs — a collection of Perl tools for next-generation sequencing [MIRROR]
Creating Consensus Tree Figures with Ancestral State Estimations in BayesTraits
a Graph-based phylogenetic tree, implemented in Javascript.
a ITIS search wrapper to be used with Petrie
Protecting from Envelope Stress: Variations on the Phage-shock-protein theme
Real-time analytics for large-scale classification of viral genome sequences using Feature Frequency Profile method
A python script that takes alignment file and builds a phylogeny tree.
Testing effects of missing data on phylogenetic inferences
Find bubbles in the Colored de Bruijn Graph to reconstruct phylogenetic trees
Fork of the ape R package mirrored at https://github.com/cran/ape and hosted at https://cran.r-project.org/web/packages/ape/
SEDNA: Spherical Exploration of Diversity using Nucleic Acid sequences
This simulates cell lineage using eSTGt, reconstructs the lineage tree based on the mutation table generated by the simulation, and finally outputs various comparison metrics between the simulation and reconstruction.
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