ihh/hg19-perl

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Language
Perl
Created almost 14 years ago
Updated almost 14 years ago

ihh/hg19-perl

ihh

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Perl scripts for munging UCSC hg19 table dumps

graphgram

Graph grammar library

dart

DNA, Amino Acid and RNA Tests

bracery

Procedural text generator, somewhat compatible with Tracery

gfftools

Perl scripts for working with the GFF format

trajectory-likelihood

Calculate indel trajectory likelihoods using methods of Miklós, Lunter & Holmes (2004), De Maio (2020), and Holmes (2020)

dnastore

Software for error-tolerant coding of information into DNA sequences using finite-state transducers.

abrowse

Multiple sequence alignment browser

bbcmicrobot-codec

A wrapper for dasm and @bbcmicrobot

zoogas

Z00 G45. A simple entropy-maximizing game on a Lotka-Volterra cellular automaton

quaff

FASTA/FASTQ alignment

pixelzoo

tree-align-view

A multiple alignment viewer with integrated phylogeny and structure browsing.

carder

Lightweight wrapper to Gajus Kuizinas' Swing for building card-swiping interactive fiction on the web.

gertie

bioe241

Materials for UC Berkeley class BioE241

stockholm-js

Parser for Stockholm format

boswell

IDE for multiplayer choice-based fiction

rnastatalign-paper

Paper: "Evolutionary Triplet Models of Structured RNA", PLoS Comp Biol 2009

funkscene

A series of interesting choices.

ihh.github.io

Holmes lab website

EvolPairHMM

Evolutionary Pair HMM

transducer-tutorial

spongelife

schooz

Scheme hypertext framework

phylogenetic-likelihood

JavaScript implementation of phylogenetic likelihood calculations

nanopair

wikimess

tag-parser

Algorithms to parse biological tree-adjoining grammars

latex-tutorial

jukes-cantor

Jukes-Cantor formula and distance matrix