NEWS.md

In shaunpwilkinson/profile: Analysis with Profile Hidden Markov Models

aphid 1.3.3 (2019-05-08)

• Fixed bug in train.HMM causing log likelihood to vanish for Baum Welch training (thanks Marie-Amelie Forin-Wiart for bug report)

• Enabled full array output for posterior.PHMM (thanks Leon Eyrich Jessen for bug report)

aphid 1.3.2 (2019-03-15)

• Specified previous version of set.seed sampler with RNGversion() calls

aphid 1.3.1 (2018-11-10)

• Fixed bug in align not closing cluster after multithread

• Fixed bug in align preventing colnames for 2-row alignments

aphid 1.3.0 (2018-10-09)

• Enabled 'near-enough' alignment matching between Viterbi iterations in train.PHMM via limit parameter

• Prevented memory overflow in 'train.PHMM' caused by md5 hash attmpt on very large alignments

• Included faster maximum entropy sequence weighting option (Henikoff & Henikoff 1994)

aphid 1.2.0 (2018-08-14)

• Enabled multithread option for Baum Welch training of profile HMMs.

• Fixed checksum parse issue in readPHMM

aphid 1.1.0

• Added posterior probabilities for PHMMs.

• derivePHMM.list seed selection changed from max length to most common length.

• Fixed issue in 'align' causing distance matrix error if seqweights not set to NULL (Thanks to Ben Margetts for bug report).

• Updated dependency list to include kmer instead of phylogram.

aphid 1.0.1

• Internalized function erroneously exported in initial CRAN release.

aphid 1.0.0

• Released on CRAN 2017-06-24.

shaunpwilkinson/profile documentation built on July 16, 2024, 9:29 a.m.