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gabe-foley-thesis/README.md

Methods for ancestral sequence reconstruction of large and complex protein families

Code repository for my thesis.

I've added these repositories here so they can stand as a permanent record alongside my thesis.

For more recent code, please see my main account -> github.com/gabefoley

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  1. bodenlab/GRASP bodenlab/GRASP Public

    Graphical Representation of Ancestral Sequence Predictions

    JavaScript 15 5

  2. bodenlab/GRASP-resources bodenlab/GRASP-resources Public

    ASR workflows & GRASP supplementary material

    Python 4

  3. SeqScrub SeqScrub Public

    Website for cleaning FASTA headers and checking for obsolete sequences.

    JavaScript

  4. Phylo_Island Phylo_Island Public

    Tool for performing phylogenetic and ancestral studies on multi-subunit proteins

    JavaScript

  5. ancestral_agreement ancestral_agreement Public

    Calculate the level of agreement between two ancestral reconstructions from differing tools

    Python

  6. ancestralcost ancestralcost Public

    Calculate the parsimony cost of having an ancestral residue implied by an alignment and tree

    Python