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Diff Rev Chgset Date Author Log Message
(edit) @583 [583] 6 weeks reed remove debugging message
(edit) @582 [582] 6 weeks reed fixed protein models
(edit) @581 [581] 8 weeks reed let's try to wag model again
(edit) @580 [580] 8 weeks reed typos
(edit) @579 [579] 2 months reed added support for output blocks
(edit) @578 [578] 3 months reed addition of new protein models
(edit) @577 [577] 3 months reed added paml2dawg R program to transform paml matrices to dawg matrices
(edit) @576 [576] 3 months reed residue model
(edit) @575 [575] 3 months reed typo
(edit) @574 [574] 3 months reed gcc doesn't like char in right_align, use string (see previous commit)
(edit) @573 [573] 3 months reed framework for aa models
(edit) @572 [572] 3 months reed append and split options implemented
(edit) @571 [571] 3 months reed new command line options compiling fix on windows
(edit) @570 [570] 3 months reed code comments
(edit) @569 [569] 3 months reed use uniform scale
(edit) @568 [568] 3 months reed typos; bugfixes; wagstar
(edit) @567 [567] 3 months reed amion acid model; woot
(edit) @566 [566] 3 months reed star wag model
(edit) @565 [565] 3 months reed aagtr model
(edit) @564 [564] 3 months reed simplify substitution headers
(edit) @563 [563] 3 months reed gapoverlap of root controls entire section
(edit) @562 [562] 3 months reed cache some alignment information
(edit) @561 [561] 3 months reed check for spirit 2.2
(edit) @560 [560] 3 months reed output formats
(edit) @559 [559] 3 months reed obey arg.output
(edit) @558 [558] 3 months reed output work; sequence header
(edit) @557 [557] 3 months reed bug fix
(edit) @556 [556] 3 months reed removed is_singular warning
(edit) @555 [555] 3 months reed compiling on windows and with boost 1.42
(edit) @554 [554] 3 months reed don't need to look for bison and flex
(edit) @553 [553] 3 months reed output class
(edit) @552 [552] 3 months reed begin creating output class
(edit) @551 [551] 3 months reed begin creating output class
(edit) @550 [550] 4 months reed bug fix related to deleted sites
(edit) @549 [549] 4 months reed do not compile old files
(edit) @548 [548] 4 months reed tree scaling supported
(edit) @547 [547] 4 months reed limit alignment to output sequences
(edit) @546 [546] 4 months reed thoughts on using boost::regex
(edit) @545 [545] 4 months reed use boost::sub_range
(edit) @544 [544] 4 months reed input file aliases
(edit) @543 [543] 4 months reed option to remove empty gaps
(edit) @542 [542] 4 months reed only one root per segment
(edit) @541 [541] 4 months reed algo for removing empty columns
(edit) @540 [540] 4 months reed LowerCase? and MarkIns? segment options
(edit) @539 [539] 4 months reed new residue exchange model
(edit) @538 [538] 4 months reed replicates; new rex interfance
(edit) @537 [537] 4 months reed autonaming of sections using [[-]] works
(edit) @536 [536] 4 months reed start work on makeing [[-]] an autonamed section
(edit) @535 [535] 4 months reed don't allow section headers to be empty (Reversion)
(edit) @534 [534] 4 months reed replaced several usages of maps with vectors and precached indices
(edit) @533 [533] 4 months reed changed support for internal and hidden labels
(edit) @532 [532] 4 months reed work on indexing node labels
(edit) @531 [531] 4 months reed simplifed pile whitespace
(edit) @530 [530] 4 months reed comments in pile format should eend at eoi as well
(edit) @529 [529] 4 months reed branch_color now updated properly
(edit) @528 [528] 4 months reed whitespace cleanup
(edit) @527 [527] 4 months reed code reform
(edit) @526 [526] 4 months reed patched together a working aligner
(edit) @525 [525] 4 months reed alignment type
(edit) @524 [524] 4 months reed more bug fixes; Sim.Seed supports arrays
(edit) @523 [523] 4 months reed compiling issues; assert bug; NULL and empty string same as - for cin …
(edit) @522 [522] 4 months reed continued work on building new interface
(edit) @521 [521] 5 months jawley add GetValue? and GetTextValue? functions
(edit) @520 [520] 6 months reed compilation
(edit) @519 [519] 6 months reed more work
(edit) @518 [518] 6 months reed move evolution functions
(edit) @517 [517] 6 months reed stat porting algorithm to matic
(edit) @516 [516] 6 months reed changes for compling on windows
(edit) @515 [515] 6 months reed minor stuff
(edit) @514 [514] 6 months reed fix for compiling on linux
(edit) @513 [513] 6 months jawley minor changes
(edit) @512 [512] 6 months jawley fixed vint and vdouble
(edit) @511 [511] 6 months jawley added block and vector
(edit) @510 [510] 6 months reed more dawg work
(edit) @509 [509] 6 months reed work on matic
(edit) @508 [508] 6 months reed begin working on finishing matic
(edit) @507 [507] 6 months reed changed location of foreach.h
(edit) @506 [506] 6 months jawley add int.h int.cpp
(edit) @505 [505] 6 months jawley added int.cpp int.h changed default window size to 600*600 changed …
(edit) @504 [504] 7 months jawley
(edit) @503 [503] 7 months reed pile sections are now as a vector, not a map
(edit) @502 [502] 7 months reed conversion of pile to ma almost done; vecio utility added
(edit) @501 [501] 7 months reed some more work on from_pile
(edit) @500 [500] 7 months reed first phase of converting dawg::pile into a vector of dawg::ma's
(edit) @499 [499] 7 months reed stream parsing
(edit) @498 [498] 7 months reed added foreach.h wrapper
(edit) @497 [497] 7 months reed XCMD -> XM
(edit) @496 [496] 7 months reed change filename
(edit) @495 [495] 7 months reed missing file
(edit) @494 [494] 7 months reed added missing file
(edit) @493 [493] 7 months jawley
(edit) @492 [492] 7 months reed whitespace
(edit) @491 [491] 7 months reed conversion of pile raw format to flat format
(edit) @490 [490] 7 months reed add std::string parser to wood
(edit) @489 [489] 7 months reed use omit to prevent auto-assignment
(edit) @488 [488] 7 months reed another typo
(edit) @487 [487] 7 months reed typo
(edit) @486 [486] 7 months reed typo
(edit) @485 [485] 7 months reed typos
(edit) @484 [484] 7 months reed white_space parser lexeme id
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