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matsen (Erick Matsen)

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Name: Erick Matsen

Member Since: Aug 06, 2009 (4 months)

3 public repos
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Following 0 githubbers and watching 3 repositories view all →

Public Repositories (3)

- 1
- 1
common

Erick's commonly used ocaml files

Last updated Mon Dec 14 11:34:52 -0800 2009
- 1
- 1
pplacer

phylogenetic placement tool

Last updated Mon Dec 14 11:33:43 -0800 2009
- 1
- 1
constnj

code to accompany "constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pai...

Last updated Mon Nov 16 21:38:23 -0800 2009

Public Activity

matsen pushed to master at matsen/common Mon Dec 14 11:34:52 -0800 2009

HEAD is f3d13f691f4b2cdd5d956da2ec64494fc665e76c x

matsen committed f3d13f69:

added MatrixFuns.iterij

matsen pushed to master at matsen/pplacer Mon Dec 14 11:33:44 -0800 2009

HEAD is c23999d4492b1f7c0a37af07a723ca7ce64297d8 x

4 commits »

matsen committed c23999d4:

comments
matsen committed c72691f0:

fantasy optimization now working
matsen committed 198998be:

optimization of baseball parameters
matsen committed 580e5e1d:

added like_rax

matsen pushed to master at matsen/pplacer Mon Dec 14 07:47:56 -0800 2009

HEAD is 2d3e63d76b3b99f04e11a513f6c5daa6786f0227 x

matsen committed 2d3e63d7:

memory tracking now in GB to avoid byte word overflow problems

matsen pushed to master at matsen/common Mon Dec 14 06:34:52 -0800 2009

HEAD is 66b4183932125de38afe018d5129cf15d95ec574 x

matsen committed 66b41839:

cleanup and added mimic

matsen pushed to master at matsen/pplacer Mon Dec 14 06:33:59 -0800 2009

HEAD is 6ab69a4e11e0b53c01563ecc5e85225400e8a753 x

matsen committed 6ab69a4e:

removed old stuff from alignment_funs

matsen pushed to master at matsen/pplacer Mon Dec 14 06:30:33 -0800 2009

HEAD is 868f2622caa25e653db89658fc377a29339ec782 x

matsen committed 868f2622:

cleanup; added maximal observed memory usage; pulled out get for deDiagonalize

matsen pushed to master at matsen/pplacer Mon Dec 14 05:32:40 -0800 2009

HEAD is a5a67d743dd788852f1af846c0845c64e9930e38 x

matsen committed a5a67d74:

model now has a cache for its transition matrix

matsen pushed to master at matsen/pplacer Mon Dec 14 04:39:32 -0800 2009

HEAD is a08454cd564f8fa1a25d8e81a89b235f09abd4c3 x

matsen committed a08454cd:

glv_arr style implementation now working

matsen pushed to master at matsen/pplacer Mon Dec 14 03:41:24 -0800 2009

HEAD is fc900d1d9e6af4dbfabfe2d8e838acfd3deb5d88 x

3 commits »

matsen committed fc900d1d:

last commit before moving to a glv_arr implementation
matsen committed 6a8f1c9a:

named arguments for Glv.evolve
matsen committed 0b120a1b:

last commit before making expWithT write to a destination

matsen pushed to master at matsen/common Thu Dec 10 08:59:10 -0800 2009

HEAD is b03998023b1879f0bf9257822a262061617f868a x

matsen committed b0399802:

modified: alignment.ml

matsen pushed to master at matsen/pplacer Thu Dec 10 08:58:53 -0800 2009

HEAD is fbf8ad732af17cadbdbe740ad2a09597aa551596 x

matsen committed fbf8ad73:

now prints number of compactions

matsen pushed to master at matsen/pplacer Thu Dec 10 06:46:10 -0800 2009

HEAD is 0c945d448fd032ff4e503187ba5c939698ffaf03 x

matsen committed 0c945d44:

added memory ceiling option

matsen pushed to master at matsen/pplacer Wed Dec 09 06:10:29 -0800 2009

HEAD is 7b34bde780779aac9133d8ea38a9ec00a3149f5a x

matsen committed 7b34bde7:

moved to cycling through the queries using Fasta_channel

matsen pushed to master at matsen/pplacer Sun Dec 06 11:12:11 -0800 2009

HEAD is 88f0f9adefc3e27da0ec2d3b88e2d41fad86e262 x

2 commits »

matsen committed 88f0f9ad:

new file: fasta_channel.ml
matsen committed 22e4459c:

last commit before moving to iteration over a fasta channel

matsen pushed to master at matsen/pplacer Sat Dec 05 11:37:43 -0800 2009

HEAD is 04e856b60a6673a92757345c5a75ca0f6c6ae8cd x

2 commits »

matsen committed 04e856b6:

eliminated reading of GTR nucleotide frequencies so that we are compatible with RAxML 7.2.3. thus we always calculate frequencies from the alignment.
matsen committed 6dc77610:

cleanup

matsen pushed to master at matsen/pplacer Sat Dec 05 07:39:55 -0800 2009

HEAD is 60f66ec16b09c0ae43ed91acbdf5c1298f5df1c0 x

matsen committed 60f66ec1:

added like diff to fantasy baseball

matsen pushed to master at matsen/pplacer Sat Dec 05 06:00:26 -0800 2009

HEAD is c66f34a2bad3de4dc8937a93e0044ee1abe41909 x

matsen committed c66f34a2:

made the bounce and the fat widths agree

matsen pushed to master at matsen/pplacer Fri Dec 04 17:25:10 -0800 2009

HEAD is 6674aaa1dd4eec14a3f582cfdeed2d0bf78d6a41 x

matsen committed 6674aaa1:

deleted: makefile

matsen pushed to master at matsen/pplacer Fri Dec 04 17:14:02 -0800 2009

HEAD is cc6bce360ed127ce761f007318e6bb802002b687 x

3 commits »

matsen committed cc6bce36:

tags now written in correct order for phyloxml
matsen committed 148c27af:

cleaned up prefs
matsen committed 6d611c15:

debugging the width difference between the bounce tree and the fat tree; not done yet

matsen pushed to master at matsen/pplacer Thu Dec 03 05:18:23 -0800 2009

HEAD is 3cecdb2b82d3c4610bf7154f46323ef0d0d04a63 x

2 commits »

matsen committed 3cecdb2b:

changing names
matsen committed 860d2dc3:

changing names

matsen pushed to master at matsen/pplacer Wed Dec 02 05:56:24 -0800 2009

HEAD is 5dbab315c82a590755972175d931ab173da457e2 x

3 commits »

matsen committed 5dbab315:

added name support for phyloxml
matsen committed 7440e13b:

started n_strikes from 1
matsen committed 4108eaed:

explanatory comment for fantasy matrices

matsen pushed to master at matsen/pplacer Mon Nov 30 08:58:53 -0800 2009

HEAD is edf74fc943f99ea1a606d709e0ececb3f6ba7765 x

matsen committed edf74fc9:

fixed the fantasy ball, which was cutting out early

matsen pushed to master at matsen/pplacer Mon Nov 30 08:15:01 -0800 2009

HEAD is f5b7e9a674e32c747364ee5d2b0f071ab8542c4c x

matsen committed f5b7e9a6:

reverse video replaced with white_bg, and it works now

matsen pushed to master at matsen/pplacer Mon Nov 30 06:19:32 -0800 2009

HEAD is 17b76dfaf1355b16149350c466661df4cf633436 x

19 commits »

matsen committed 17b76dfa:

now parses RAxML v7.2.3
matsen committed 43fc34e2:

GSL error handling for fantasy
matsen committed a64926a9:

cleaned out some rate-related comments
matsen committed dafe2aad:

fantasy now has an option
matsen committed af08c076:

fantasy makes two files, nt and ba
matsen committed fa543512:

first commit with fantasy
matsen committed ff3e9d6e:

last commit before adding fantasy
matsen committed c53cb5c9:

testing ways to decrease likelihood function calls
matsen committed 0510e16e:

friends now more intelligent with respect to ratio cutoff
matsen committed 59ff532e:

friend acceleration operational
matsen committed 102f93b4:

last commit before putting in the similarity-based acceleration
matsen committed 10bbdcd2:

int_approx_find
matsen committed 29faddc5:

modified: ltrie.ml
matsen committed 96807a67:

ltrie uses option
matsen committed fb4edf76:

ltrie operational
matsen committed ced42ebe:

ltrie attempt #2
matsen committed 8182f58d:

ltrie using Hashtbl, about to move to Map
matsen committed 71ac986f:

cut out entropy
matsen committed 5ab5a34b:

cut out entropy

matsen pushed to dev at matsen/pplacer Sun Nov 29 10:16:44 -0800 2009

HEAD is af08c076f4de9f8e6fbb3ab2c9560516e22ca3de x

matsen committed af08c076:

fantasy makes two files, nt and ba

matsen pushed to dev at matsen/pplacer Sun Nov 29 10:08:12 -0800 2009

HEAD is fa54351214c9444ce3fb6385e1d8a01780df2e8c x

matsen committed fa543512:

first commit with fantasy

matsen pushed to dev at matsen/pplacer Sun Nov 29 08:41:32 -0800 2009

HEAD is ff3e9d6e64a2aa9ead3270fa5487e5c49d78c876 x

matsen committed ff3e9d6e:

last commit before adding fantasy

matsen pushed to master at matsen/common Fri Nov 27 12:15:09 -0800 2009

HEAD is 095e61fcdc854235e71724a27fec50eb7ab5f793 x

matsen committed 095e61fc:

added seconds to timing

matsen pushed to dev at matsen/pplacer Fri Nov 27 11:57:20 -0800 2009

HEAD is c53cb5c9ba23bc8ca8bddf8b3c4d1fee7a319af8 x

2 commits »

matsen committed c53cb5c9:

testing ways to decrease likelihood function calls
matsen committed 0510e16e:

friends now more intelligent with respect to ratio cutoff