vaporware computational molecular evolution command line suite
using small sqlite databases for input and output
- mclr : Monte Carlo likelihood ratio
- bp : 'blinking process'
- ec : endpoint-conditioned (or leaf-conditioned for trees)
- ctmc : continuous-time Markov chain (often required to be time-reversible)
- mmpp : Markov modulated Poisson process
tree:
$ sqlite3 brown.tree.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE blen (edge integer, blen real, primary key (edge));
CREATE TABLE taxa (node integer, name text, primary key (node));
CREATE TABLE topo (edge integer, va integer, vb integer, primary key (edge));
sqlite>
rate matrix:
$ sqlite3 rate.matrix.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE distn (state integer, prob real, primary key (state));
CREATE TABLE rates (source integer, sink integer, rate real, primary key (source, sink));
CREATE TABLE states (state integer, name text, primary key (state));
sqlite>
single sampled substitution history on a tree
$ sqlite3 history.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE history (segment integer, va integer, vb integer, blen real, state integer, primary key (segment));
sqlite>
multiple sampled substitution histories on a tree
$ sqlite3 histories.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE histories (history integer, segment integer, va integer, vb integer, blen real, state integer, primary key (history, segment));
sqlite>
multiple sampled substitution histories on a tree, per alignment column
$ echo ".schema" | sqlite3 test.samples.db
CREATE TABLE histories (history integer, offset integer, segment integer, va integer, vb integer, blen real, state integer, primary key (history, offset, segment));
2d vertex layout:
$ sqlite3 layout.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE layout (node integer, x real, y real, primary key (node));
sqlite>
segmentation of a sampled history into contiguous isostate regions:
$ sqlite3 segmentation.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE bipartite (isostate integer, parity integer, primary key (isostate));
CREATE TABLE isostate (segment integer, isostate integer, primary key (segment));
sqlite>
genetic code:
$ sqlite3 universal.code.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE code (state integer, residue text, codon text, primary key (state));
sqlite>
a single path (not tree) endpoint-conditioned history sample:
$ sqlite3 pathsample.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE history (segment integer, state integer, blen real, primary key (segment));
sqlite>
multiple path (not tree) endpoint-conditioned history samples:
$ sqlite3 pathsamples.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE histories (history integer, segment integer, state integer, blen real, primary key (history, segment));
sqlite>
endpoint-conditioned expectations from a time-reversible rate matrix:
$ sqlite3 expectations.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE usage (initial integer, final integer, source integer, sink integer, usage real, primary key (initial, final, source, sink));
CREATE TABLE wait (initial integer, final integer, state integer, wait real, primary key (initial, final, state));
sqlite>
an alignment sampled at nodes related by an unrooted tree, using a time-reversible continuous Markov process:
$ sqlite3 sampled.alignment.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE alignment (offset integer, taxon integer, state integer, primary key (offset, taxon));
sqlite>
site patterns, with multiplicities, extracted from an alignment:
$ sqlite3 patterns.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE multiplicities (pattern integer, multiplicity integer, primary key (pattern));
CREATE TABLE patterns (pattern integer, taxon integer, state integer, primary key (pattern, taxon));
sqlite>
full history sample of a complicated reversible Markov process on a path:
$ sqlite3 blink.path.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE blink_history (part integer, segment integer, state integer, duration real, primary key (part, segment));
CREATE TABLE primary_history (segment integer, state integer, duration real, primary key (segment));
sqlite>
log likelihoods under a model, for multiple path histories:
$ sqlite3 log.likelihoods.db
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite> .schema
CREATE TABLE log_likelihoods (history integer, log_likelihood real, primary key (history));
sqlite>
p53 tumor data:
$ echo ".schema" | sqlite3 cancer/tumor.db
CREATE TABLE tumor (offset integer, wild_state integer, mutant_state integer, primary key (offset, wild_state, mutant_state));