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align_agree

Align 2 alignments (with identical sets of sequences) using Needleman-Wunsch. Column-column score is number of identical non-gap residues.

ants

Langton's ant with various generalizations. (java script)

collatz

Scripts for studying collatz problem and some generalizations.

genotype_simulations

Simulate genotypes with various relationships (parent-child, full sibling, 1st cousing, unrelated, ...) ... To study strategies for identifying close relatives in a large set of genotypes.

genotypes_graph

Classes implementing a graph, and nodes representing genotypes to (hopefully) allow efficiently searching for the genotype in the graph which is most similar to another genotype.

go

my go (go lang) code

go-genotype-search

go language implementation of search for similar genotype sequences.

gtsimsrch

histogram

Histogramming data and plotting resulting histograms.

interactive_kenken

Kenken where the player defines the cages and the operations in each.

js_factorsquarepuzzles

javascript for interactive 'factor square' puzzle.

mb

perl modules and scripts for running mrbayes and analyzing output.

mcmc_toy

MCMC and MCMCMC. Space is [0..N]^d , proposals are symmetric.

mcmctoy_simruns

Simulation run output from mcmc_toy.

my_mdl

This is my version of Ane's 'mdl' a program to partition a long alignment into a set of shorter 'groups' according to the criterion of Minimum Description Length (MDL).

mymrbayes

A version of MrBayes (starting from 3.2.4) with some features added by me.

orthologger

Perl modules and scripts to analyze gene families and find orthologs by aligning, constructing trees, rooting them by mindl wrt a given species tree, and identifying speciation nodes of tree.

patterns

Various svg files with e.g. puzzle shapes to make with pentiamonds and tetrahexes.

pedigree_test

test correctness of parents specified in pedigree by comparing genotypes.

pentominosolver

raaz_classifier

perl code for constructing histograms and classifiers using mcmc techniques.

randommathproblems

Perl modules to generate randomized math problems of various types. The idea is that each module generates problems of a certain type, but with the specific numbers involved chosen randomly. So that every student an be given a set of problems different from everyone else's, to avoid the problem of some students copying other students' answers.

sgn

The code behind the Sol Genomics Network main website

simgtsrch

C code to find similar genotype sets.

stringart

Perl script(s?) to string-art style drawings.

svgpatternmaker

Perl modules and scripts for generating svg for various patterns (e.g. honeycomb)

test

just for practice

tomfy.github.io

tree_reconstruction

simulate alignments from a tree and reconstruct with raxml to study how well can reconstruct.

tree_reconstruction_studies

Tree_reconstruction_studies