---
name: "Bio::Tools::Run::Phylo::Phylip::Base"
section: "3pm"
platform: "linux"
package: "libbio-perl-run-perl"
version: "1.7.3-13"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Tools::Run::Phylo::Phylip::Base"
---

# Bio::Tools::Run::Phylo::Phylip::Base(3pm)

Base object for Phylip modules

## NAME

Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules

## SYNOPSIS

\# Do not use directly # This module is for setting basic data sets for the Phylip wrapper # modules

## DESCRIPTION

This module is just a base object for Bioperl Phylip wrappers.

IMPORTANT PHYLIP VERSION ISSUES By default we assume you have Phylip 3.6 installed, if you have installed Phylip 3.5 you need to set the environment variable PHYLIPVERSION

## 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:

```
  http://redmine.open-bio.org/projects/bioperl/
```

## 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::Tools::Run::Phylo::Phylip::Base->new();
 Function: Builds a new Bio::Tools::Run::Phylo::Phylip::Base object
 Returns : an instance of Bio::Tools::Run::Phylo::Phylip::Base
 Args    :
```

### outfile

```
 Title   : outfile
 Usage   : $obj->outfile($newval)
 Function: Get/Set default PHYLIP outfile name ('outfile' usually)
           Changing this is only necessary when you have compiled
           PHYLIP to use a different filename for the default 'outfile'
           This will not change the default output filename by
           PHYLIP
 Returns : value of outfile
 Args    : newvalue (optional)
```

### treefile

```
 Title   : treefile
 Usage   : $obj->treefile($newval)
 Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
 Returns : value of treefile
 Args    : newvalue (optional)
```

### fontfile

```
 Title   : fontfile
 Usage   : $obj->fontfile($newval)
 Function: Get/Set the fontfile
 Returns : value of fontfile (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```

### plotfile

```
 Title   : plotfile
 Usage   : $obj->plotfile($newval)
 Function: Get/Set the plotfile
 Returns : value of plotfile (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```

### version

```
 Title   : version
 Usage   : $obj->version($newval)
 Function: Get/Set the version
 Returns : value of version (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
```