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2009-11-21	paradis	last changes for ape 2.4-1	commit \| commitdiff \| tree
2009-11-10	paradis	removing plot.phylo.coor (definitely)	commit \| commitdiff \| tree
2009-11-10	paradis	again...........	commit \| commitdiff \| tree
2009-11-03	paradis	changed rtree and rcoal	commit \| commitdiff \| tree
2009-10-28	paradis	some bug fixes	commit \| commitdiff \| tree
2009-10-05	paradis	final changes for ape 2.4 including removing mlphylo!	commit \| commitdiff \| tree
2009-10-02	paradis	various changes and fixes	commit \| commitdiff \| tree
2009-09-30	paradis	final plot.phylo and change to BOTHlabels() from Janet...	commit \| commitdiff \| tree
2009-09-24	paradis	finally the new plot.phylo...	commit \| commitdiff \| tree
2009-09-18	paradis	removing files that have moved to pegas	commit \| commitdiff \| tree
2009-09-18	paradis	moved functions from ape to pegas -> ape 2.4	commit \| commitdiff \| tree
2009-09-16	paradis	bug fix in seg.sites + new option in base.freq	commit \| commitdiff \| tree
2009-09-14	paradis	typo fixing...	commit \| commitdiff \| tree
2009-09-09	paradis	a collection of bug fixes	commit \| commitdiff \| tree
2009-07-27	paradis	fixing write.nexus()	commit \| commitdiff \| tree
2009-07-27	paradis	fixing zoom()	commit \| commitdiff \| tree
2009-07-23	paradis	fixing add.scale.bar()	commit \| commitdiff \| tree
2009-07-20	paradis	faster nj()!!!	commit \| commitdiff \| tree
2009-07-14	paradis	fixing nj() with many 0 distances	commit \| commitdiff \| tree
2009-07-07	paradis	several bug fixes while in JKT	commit \| commitdiff \| tree
2009-06-23	paradis	fixes for ape 2.3-1	commit \| commitdiff \| tree
2009-06-23	paradis	fix a bug in drop.tip + add new option 'rooted'	commit \| commitdiff \| tree
2009-06-19	paradis	new is.monophyletic() + various changes/fixes	commit \| commitdiff \| tree
2009-06-12	paradis	removed klastorin()	commit \| commitdiff \| tree
2009-06-10	paradis	improved ace()	commit \| commitdiff \| tree
2009-06-09	paradis	fixed null model in yule.cov + various things	commit \| commitdiff \| tree
2009-05-19	paradis	new c.DNAbin()	commit \| commitdiff \| tree
2009-05-14	paradis	faster rcoal... at last!	commit \| commitdiff \| tree
2009-05-12	paradis	many changes.......	commit \| commitdiff \| tree
2009-04-27	paradis	fixed a small bug in read.tree	commit \| commitdiff \| tree
2009-04-01	paradis	fix on dist.gene + a few man pages corrections	commit \| commitdiff \| tree
2009-03-30	paradis	various changes for ape 2.3	commit \| commitdiff \| tree
2009-03-27	paradis	added edge.lty to plot.phylo	commit \| commitdiff \| tree
2009-03-23	paradis	adding contribs by Daniel Lawson	commit \| commitdiff \| tree
2009-03-23	paradis	change nlm to nlminb in ace() + new makeNodeLabel ...	commit \| commitdiff \| tree
2009-03-10	paradis	various fixes + del xenarthra	commit \| commitdiff \| tree
2009-03-04	paradis	correcting bug in drop.tip	commit \| commitdiff \| tree
2009-02-20	paradis	added the contribution of PL on CDAM	commit \| commitdiff \| tree
2009-02-20	paradis	new yule.time + several corrections in man pages	commit \| commitdiff \| tree
2009-01-20	paradis	fix to avoid uncessary warning in ace(method = "GLS")	commit \| commitdiff \| tree
2009-01-19	paradis	bug fix in read.nexus + new ?ape man page	commit \| commitdiff \| tree
2009-01-13	paradis	correcting errors in Rd files	commit \| commitdiff \| tree
2009-01-12	paradis	updates for ape 2.2-3	commit \| commitdiff \| tree
2009-01-08	paradis	various updates + adding SPR+TBR in fastme.bal()	commit \| commitdiff \| tree
2008-12-20	paradis	bug fixed in ltt.plot.R	commit \| commitdiff \| tree
2008-11-24	paradis	fix bug in read.nexus()	commit \| commitdiff \| tree
2008-11-04	paradis	fixing bug in chronopl(, CV = TRUE)	commit \| commitdiff \| tree
2008-10-09	paradis	improved cbind.DNAbin for ape 2.2-2	commit \| commitdiff \| tree
2008-10-08	paradis	updated phymltest() for PhyML 3.0 + changed rbind.DNAbin()	commit \| commitdiff \| tree
2008-10-02	paradis	bug corrected in del.gaps + small change in man page...	commit \| commitdiff \| tree
2008-09-25	paradis	correcting ref in mcmc.popsize.Rd (from Gramlitz)	commit \| commitdiff \| tree
2008-09-18	paradis	fix a few bugs + correct some the man page of sh.test()	commit \| commitdiff \| tree
2008-07-28	paradis	changed some data sets (made lighter) + clarified man...	commit \| commitdiff \| tree
2008-07-21	paradis	adding tree_build.c	commit \| commitdiff \| tree
2008-07-18	paradis	correcting 2 bugs in new dist.gene()	commit \| commitdiff \| tree
2008-07-18	paradis	fixed prop.part()	commit \| commitdiff \| tree
2008-07-18	paradis	new dist.gene() + corrected mlphylo()	commit \| commitdiff \| tree
2008-07-11	paradis	fixed sh.test() for ape 2.2-1	commit \| commitdiff \| tree
2008-07-11	paradis	final fix in read.nexus() for ape 2.2-1	commit \| commitdiff \| tree
2008-07-09	paradis	bug fix in read.nexus()	commit \| commitdiff \| tree
2008-07-08	paradis	various corrections	commit \| commitdiff \| tree
2008-07-03	paradis	new makeLabel() + modifs in read.dna() & write.dna()	commit \| commitdiff \| tree
2008-06-28	paradis	changed check.labels = TRUE in dist.topo() and consensus()	commit \| commitdiff \| tree
2008-06-24	paradis	bug fix in read.nexus()	commit \| commitdiff \| tree
2008-06-19	paradis	bug fix in collapsed.singles()	commit \| commitdiff \| tree
2008-06-18	paradis	bugs fixing in mlphylo()	commit \| commitdiff \| tree
2008-06-12	paradis	bug fix in root()	commit \| commitdiff \| tree
2008-06-09	paradis	improved unique.multiPhylo()	commit \| commitdiff \| tree
2008-06-08	paradis	adding del.gaps()	commit \| commitdiff \| tree
2008-05-08	paradis	doc for corBlomberg	commit \| commitdiff \| tree
2008-05-08	paradis	final wrap of ape 2.2	commit \| commitdiff \| tree
2008-05-06	paradis	cosmetic modif on rtree() + last (?) changes to Damien...	commit \| commitdiff \| tree
2008-04-24	paradis	fix bug in seg.sites + improved Damien's man pages	commit \| commitdiff \| tree
2008-04-18	paradis	added corPagel + gave version # 2.2	commit \| commitdiff \| tree
2008-04-17	paradis	fix on drop.tip()	commit \| commitdiff \| tree
2008-04-17	paradis	new files by Damien + a few bug fixes	commit \| commitdiff \| tree
2008-04-10	paradis	removed the print(node.labels)	commit \| commitdiff \| tree
2008-03-31	paradis	improved chronopl	commit \| commitdiff \| tree
2008-03-17	paradis	fixed bugs in multi2di and di2multi + code and doc...	commit \| commitdiff \| tree
2008-03-11	paradis	code clean-up in DNA.R	commit \| commitdiff \| tree
2008-03-03	paradis	update for ape 2.1-2	commit \| commitdiff \| tree
2008-02-27	paradis	fixing a few bugs...	commit \| commitdiff \| tree
2008-02-13	paradis	improved root()	commit \| commitdiff \| tree
2008-02-08	paradis	added "DUP=FALSE, NAOK=TRUE" to .C in DNA.R	commit \| commitdiff \| tree
2008-02-07	paradis	various updates...[21~	commit \| commitdiff \| tree
2008-01-21	paradis	fix a bug in nuc.div()	commit \| commitdiff \| tree
2008-01-14	paradis	conversion tree -> phylo	commit \| commitdiff \| tree
2008-01-14	paradis	stabler and faster C code for ME and BIONJ	commit \| commitdiff \| tree
2008-01-08	paradis	new function rmtree	commit \| commitdiff \| tree
2008-01-04	paradis	current 2.1 release	commit \| commitdiff \| tree

Local fork of ape (analysis of ecology)

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