---
name: "Bio::Align::ProteinStatistics"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Align::ProteinStatistics"
---

# Bio::Align::ProteinStatistics(3pm)

Calculate Protein Alignment statistics (mostly distances)

## NAME

Bio::Align::ProteinStatistics - Calculate Protein Alignment statistics (mostly distances)

## SYNOPSIS

```
  use Bio::Align::ProteinStatistics;
  use Bio::AlignIO;
  my $in = Bio::AlignIO->new(-format => 'fasta',
                            -file   => 'pep-104.fasaln');
  my $aln = $in->next_aln;
  my $pepstats = Bio::Align::ProteinStatistics->new();
  $kimura = $protstats->distance(-align => $aln,
                                 -method => 'Kimura');
  print $kimura->print_matrix;
```

## DESCRIPTION

This object is for generating various statistics from a protein alignment.  Mostly it is where pairwise protein distances can be calculated.

## REFERENCES

D\_Kimura - Kimura, M. 1983. The Neutral Theory of Molecular Evolution. CUP, \
            Cambridge.

## FEEDBACK

### Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list.  Your participation is much appreciated.

```
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
```

### Support

Please direct usage questions or support issues to the mailing list:

*bioperl-l@bioperl.org*

rather than to the module maintainer directly. Many experienced and  reponsive experts will be able look at the problem and quickly  address it. Please include a thorough description of the problem  with code and data examples if at all possible.

### Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

```
  https://github.com/bioperl/bioperl-live/issues
```

## AUTHOR - Jason Stajich

Email jason-at-bioperl.org

## APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_

### new

```
 Title   : new
 Usage   : my $obj = Bio::Align::ProteinStatistics->new();
 Function: Builds a new Bio::Align::ProteinStatistics object
 Returns : an instance of Bio::Align::ProteinStatistics
 Args    :
```

### distance

```
 Title   : distance
 Usage   : my $distance_mat = $stats->distance(-align  => $aln,
                                               -method => $method);
 Function: Calculates a distance matrix for all pairwise distances of
           sequences in an alignment.
 Returns : L<Bio::Matrix::PhylipDist> object
 Args    : -align  => Bio::Align::AlignI object
           -method => String specifying specific distance method
                      (implementing class may assume a default)
```

### available\_distance\_methods

```
 Title   : available_distance_methods
 Usage   : my @methods = $stats->available_distance_methods();
 Function: Enumerates the possible distance methods
 Returns : Array of strings
 Args    : none
```

### D - distance methods

### D\_Kimura

```
 Title   : D_Kimura
 Usage   : my $matrix = $pepstats->D_Kimura($aln);
 Function: Calculate Kimura protein distance (Kimura 1983) which
           approximates PAM distance
           D = -ln ( 1 - p - 0.2 * p^2 )
 Returns : L<Bio::Matrix::PhylipDist>
 Args    : L<Bio::Align::AlignI>
```

### Data Methods

### pairwise\_stats

```
 Title   : pairwise_stats
 Usage   : $obj->pairwise_stats($newval)
 Function:
 Returns : value of pairwise_stats
 Args    : newvalue (optional)
```