hmmbuild结果文件解读：hmm文件

nseq：hmmbuild训练的序列条数110；
alen：比对的氨基酸数量256；
mlen：比对上的氨基酸数量256；
gap=alen-mlen=256-256=0;
eff_nseq:比对效率0.70；
re/pos: 相对熵0.589，又被称为KL散度(Kullback–Leibler divergence，KLD) Kullback–Leibler divergence。它表示2个函数或概率分布的差异性：差异越大则相对熵越大，差异越小则相对熵越小，特别地，若2者相同则熵为0。

A profile file consists of one or more profiles. Each profile starts with a format version identifier (here, HMMER3/f) and ends with // on a line by itself. The format version identifier allows backward compatibility as the HMMER software evolves: it tells the parser this file is from HMMER3’s save file format version f.3 The closing // allows multiple profiles to be concatenated.

LENG： Model length; a positive nonzero integer, is the number of match states in the model. Mandatory

NSEQ ： Sequence number; is a nonzero positive integer, the number of sequences that the HMM was trained on. This field is only used for logging purposes. Optional.

CKSUM Training alignment checksum; is a nonnegative unsigned 32-bit integer. This number is calculated from the training sequence data, and used in conjunction with the alignment map information to verify that a given alignment is indeed the alignment that the map is for. Optional.

EFFN ： Effective sequence number; is a nonzero positive real,
the effective total number of sequences determined by hmmbuild during sequence weighting, for combining observed counts with Dirichlet prior information in parameterizing the model.
This field is only used for logging purposes. Optional.

STATS Statistical parameters needed for E-value calculations.
is the model’s alignment mode configuration: currently only LOCAL is recognized.

is the name of the score distribution: currently MSV, VITERBI, and FORWARD are recognized.

and are two real-valued parameters controlling location and slope of each distribution, respectively;
µ and λ for Gumbel distributions for MSV and Viterbi scores, and τ and λ for exponential tails for Forward scores.

λ values must be positive. All three lines or none of them must be present: when all three are present, the model is considered to be calibrated for E-value statistics. Optional.

hmmer使用手册

基因家族分析

熵、交叉熵和相对熵的区别与联系

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