estwise - options: model

-init

[default/global/local/wing] (see section 4.3.3) For protein sequences the default is to be local (like smith waterman). For protein profile HMMs, the default is read from the HMM - the HMM carries this information internally. The global mode is equivalent to to the ls building option (the default in the HMMer2 package). The local mode is equivalent to to the fs building option (-f) in the HMMer2 package. The wing model is local on the edges and global in the middle.

-codon

[codon.table] Codon file. The default is for the universal code, but you can supply your own

-subs

[0.01] Substitution error rate, ie the assummed probability of base substitutions in the sequencing reaction/assembly that provided the DNA sequence. The substituion error is what dominates the penalty for stop codons - a higher error rate implies a smaller penalty for stop codons

-indel

[0.01] Insertion/deletion error rate, ie the assummed probability of indel events in the sequencing reaction/assembly that provided the DNA sequence. The indel rate is what provides the penalty for frameshift errors. A higher error rate implies a smaller penalty for indels.

-null

[syn/flat] Random Model as synchronous or flat [default syn] whether to use a null model which is a simple base distribution (called flat), or imagine that the viterbi path is being compared to a gene based null model that is making all the same gene exon/intron boundaries (synchronous). The latter is basically a hack which demphaises the placement of frameshifts and tries to trust the homology machinery. (not ideal!)

-alg

[333,333L,333F] Algorithm used. 333 is the normal algorithm. 333L is the looping algorithm

-kbyte

[ 2000] Max number of kilobytes used in main calculation

-pretty

show pretty ascii output as in genewise

-para

show parameters

-sum

show summary information as in genewise

-alb

show logical AlnBlock alignment, debugging output

-pal

show raw matrix alignment, debugging output

-block

[50] Length of main block in pretty output - the length of the main text in the pretty output

-divide

[//] divide string for multiple outputs, the string used to separate multiple outputs