source: @ 569

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Diff Rev Age Author Log Message
(edit) @569   5 months reed use uniform scale
(edit) @568   5 months reed typos; bugfixes; wagstar
(edit) @567   5 months reed amion acid model; woot
(edit) @566   5 months reed star wag model
(edit) @565   5 months reed aagtr model
(edit) @564   5 months reed simplify substitution headers
(edit) @563   5 months reed gapoverlap of root controls entire section
(edit) @562   5 months reed cache some alignment information
(edit) @561   5 months reed check for spirit 2.2
(edit) @560   5 months reed output formats
(edit) @559   5 months reed obey arg.output
(edit) @558   5 months reed output work; sequence header
(edit) @557   5 months reed bug fix
(edit) @556   5 months reed removed is_singular warning
(edit) @555   5 months reed compiling on windows and with boost 1.42
(edit) @554   5 months reed don't need to look for bison and flex
(edit) @553   5 months reed output class
(edit) @552   5 months reed begin creating output class
(edit) @551   5 months reed begin creating output class
(edit) @550   5 months reed bug fix related to deleted sites
(edit) @549   5 months reed do not compile old files
(edit) @548   5 months reed tree scaling supported
(edit) @547   5 months reed limit alignment to output sequences
(edit) @546   5 months reed thoughts on using boost::regex
(edit) @545   5 months reed use boost::sub_range
(edit) @544   5 months reed input file aliases
(edit) @543   5 months reed option to remove empty gaps
(edit) @542   5 months reed only one root per segment
(edit) @541   5 months reed algo for removing empty columns
(edit) @540   5 months reed LowerCase? and MarkIns? segment options
(edit) @539   5 months reed new residue exchange model
(edit) @538   5 months reed replicates; new rex interfance
(edit) @537   5 months reed autonaming of sections using -? works
(edit) @536   5 months reed start work on makeing -? an autonamed section
(edit) @535   5 months reed don't allow section headers to be empty (Reversion)
(edit) @534   5 months reed replaced several usages of maps with vectors and precached indices
(edit) @533   5 months reed changed support for internal and hidden labels
(edit) @532   5 months reed work on indexing node labels
(edit) @531   5 months reed simplifed pile whitespace
(edit) @530   5 months reed comments in pile format should eend at eoi as well
(edit) @529   5 months reed branch_color now updated properly
(edit) @528   5 months reed whitespace cleanup
(edit) @527   5 months reed code reform
(edit) @526   5 months reed patched together a working aligner
(edit) @525   5 months reed alignment type
(edit) @524   5 months reed more bug fixes; Sim.Seed supports arrays
(edit) @523   5 months reed compiling issues; assert bug; NULL and empty string same as - for cin …
(edit) @522   5 months reed continued work on building new interface
(edit) @521   6 months jawley add GetValue? and GetTextValue? functions
(edit) @520   7 months reed compilation
(edit) @519   7 months reed more work
(edit) @518   7 months reed move evolution functions
(edit) @517   7 months reed stat porting algorithm to matic
(edit) @516   7 months reed changes for compling on windows
(edit) @515   7 months reed minor stuff
(edit) @514   7 months reed fix for compiling on linux
(edit) @513   7 months jawley minor changes
(edit) @512   7 months jawley fixed vint and vdouble
(edit) @511   7 months jawley added block and vector
(edit) @510   8 months reed more dawg work
(edit) @509   8 months reed work on matic
(edit) @508   8 months reed begin working on finishing matic
(edit) @507   8 months reed changed location of foreach.h
(edit) @506   8 months jawley add int.h int.cpp
(edit) @505   8 months jawley added int.cpp int.h changed default window size to 600*600 changed …
(edit) @504   8 months jawley
(edit) @503   8 months reed pile sections are now as a vector, not a map
(edit) @502   8 months reed conversion of pile to ma almost done; vecio utility added
(edit) @501   8 months reed some more work on from_pile
(edit) @500   8 months reed first phase of converting dawg::pile into a vector of dawg::ma's
(edit) @499   8 months reed stream parsing
(edit) @498   8 months reed added foreach.h wrapper
(edit) @497   8 months reed XCMD -> XM
(edit) @496   8 months reed change filename
(edit) @495   8 months reed missing file
(edit) @494   8 months reed added missing file
(edit) @493   8 months jawley
(edit) @492   8 months reed whitespace
(edit) @491   9 months reed conversion of pile raw format to flat format
(edit) @490   9 months reed add std::string parser to wood
(edit) @489   9 months reed use omit to prevent auto-assignment
(edit) @488   9 months reed another typo
(edit) @487   9 months reed typo
(edit) @486   9 months reed typo
(edit) @485   9 months reed typos
(edit) @484   9 months reed white_space parser lexeme id
(edit) @483   9 months reed vectorize lines
(edit) @482   9 months reed allow blank headers
(edit) @481   9 months reed porting to spirit 2.1
(edit) @480   9 months reed work on dawg::pile config format
(edit) @479   9 months reed implementation of matic
(edit) @478   9 months reed putting the pieces together
(edit) @477   9 months reed added boost check
(edit) @476   9 months reed working demo of using dawgma.xmh to fill gui options
(edit) @475   9 months jawley
(edit) @474   9 months jawley
(edit) @473   9 months reed subst model working
(edit) @472   9 months reed started work on substitution model added binary search algorithm
(edit) @471   9 months reed fleshed out const and gamma+i rate models
(edit) @470   9 months reed added gamma and normal distributions started work on rate_model class new …
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