+ CHANGES IN APE VERSION 3.0-8
+
+
+NEW FEATURES
+
+ o ace() gains a new option 'use.expm' to use expm() from the
+ package of the same name in place of matexpo().
+
+
+BUG FIXES
+
+ o read.dna(, "fasta") may add '\r' in labels: this is fixed.
+
+
+
CHANGES IN APE VERSION 3.0-7
NEW FEATURES
- The new function chronos ..........
+ o The new function chronos estimates chronograms by penalised
+ likelihood and maximum likelihood with a completely reworked
+ code and interface. There is a new function makeChronosCalib to
+ set the calibration points easily. chronos() will eventually
+ replace chronopl().
o The new function 'where' searches patterns in DNA sequences.
o base.freq() is now faster with lists.
- as.matrix.DNAbin() ............ should be faster.... now accepts vectors,
-
- read.dna() has a new for FASTA files............. faster C code.
+ o as.matrix.DNAbin() should be faster and more efficient with
+ lists; it now accepts vectors.
o base.freq() gains an option 'all' to count all the possible bases
including the ambiguous ones (defaults to FALSE).
- o read.nexus() now writes tree names in the NEXUS file if given a
+ o write.nexus() now writes tree names in the NEXUS file if given a
list of trees with names.