INDELIBLE VERSION HISTORY:

05/05/2010 - Minor bug fix

• This bug did not affect simulations or sequence output. On very large trees the new [maxdistance] feature caused INDELible to freeze sometimes as it calculated maximum tree depth. This has been fixed.

29/03/2010 - V1.03 released

• New command [branchlengths] added which, for a given topology can create equal, ultrametric, and non-ultrametric random branch lengths.
• New command [maxdistance] added which will rescale any (ultrametric or non-ultrametric) tree to have a chosen maximum pairwise distance.
• The command [treedepth] can now be used on user-defined trees and non-ultrametric trees too. It now rescales the *maximum* root-to-tip distance on the tree.
• More information on those changes is available here.
• Please note these are new beta features and have not been tested as extensively as other areas of the program. Limited testing has uncovered no problems, however (as always) please refer to the output file trees.txt to check your trees.
• The option [output] PHYLIPT corrected to truncate file names correctly. Thanks AB and RS.
• Zero branch length warning removed, and further checks for trees missing branch lengths implemented. Thanks MZ.

06/11/2009 - Fixed warning message that was printing at the wrong time.

• INDELible was printing a warning associated with the tree-depth command (when the command was not being used) with user trees that did not assume molecular clock. This did not affect output in any way, but could have caused unnecessary concern! Thanks for pointing this out LW.

08/10/2009 - V1.02 released

• New function [treedepth] in [TREE] blocks for scaling trees to have the same depth, if desired. Thanks for the suggestion MR.
• [randomseed] command now also seeds random trees (unless [seed] command is used to overrule it in a [TREE] block).
• Random trees were labelled 1,2,.. for < 20 taxa, otherwise they were labelled S1,S2,... This inconsistency has been fixed. Taxa are now simply labelled 1,2,... Thanks for noticing this MR.
• PHYLIP formatted files didn't work with SEQBOOT because of blank lines after paup blocks in file. This has been changed. Thank you AB.
• INDELible used to set the automatic seed for the random number generator as a hash function of the system time and the number of seconds since 1970. This meant that if INDELible was run more than once in the same second, with identical control files but in different folders, then the program may have produced identical output from the different runs. The random seed hash now also uses either the working directory name or the number of milliseconds since the computer was switched on, which should solve this problem.

06/07/2009 - V1.01 released

• Genetic code now allowed to change on different branches in the tree, providing all codes on the tree share the same stop codons. Thanks for the suggestion DP.
• [printrates] command upgraded to output more useful information about non-homogenous discrete gamma models. Thanks for the suggestion DG.
• Obscure bug fixed. Non-homogenous models of continuous gamma rate variation combined, on the same guide tree, with other models that have no rate variation may have caused the whole tree to be treated as if it had no rate variation in some cases. This bug did not affect any other type of simulation in V1.00 and if affected the RATES file from the [printrates] command would indicate.

16/05/2009 - Small bug fixed

• INDELible used to print a blank line at the top of fasta formatted output files (which caused some alignment programs to crash).