- NAME
- getplen - CALCULATE TREE LENGTH

- SYNOPSIS
- DESCRIPTION
- PARAMETERS

- INPUT
- OUTPUT

- RETURN

# NAME

parsim.c - tree evaluation

Version Tag $Id: parsim.c,v 1.35 2006/02/06 19:55:46 db60 Exp $

# getplen - CALCULATE TREE LENGTH

## SYNOPSIS

        long getplen(const Branch *const barray, const long root,
        unsigned char **bmat, unsigned char **scratch,
        const long m, const long n, const long *weights);

## DESCRIPTION

Calculates the length of a tree using Fitch parsimony. In LVB, a large amount of time is spent in this function.

## PARAMETERS

### INPUT

barray

  Pointer to the first element of the array containing the tree to be evaluated.

root

  Index of the root of the tree to be evaluated. `barray`[`root`] is the root.

bmat

  Pointer to the first element in an array of pointers, each of which points to a row in the binary-encoded data matrix that will be used to calculate the length of the tree. `bmat`[0..`n`-1] must point to the first elements of encoded rows for objects 0..`n`-1 respectively. `bmat` is not const-qualified, since it is necessarily accessed through non-const-qualified pointers.

m

  The number of columns (bases) in the encoded data matrix.

n

  The number of objects in the tree, which is also the number of rows (objects) in the encoded data matrix.

weights

  Pointer to first element of an m-element array giving the weights of the sites. For each site, each change is counted the number of times given in the corresponding element of this array. For no weighting, each element of the array should be 1.

### OUTPUT

scratch

  `scratch` must point to an array of `n`-2 pointers, each of which must point to an allocated `m`-element array of unsigned char. Arrays accessible through `scratch` are used for temporary storage and have meaningless contents on return.

## RETURN

Returns total changes in all characters for the tree accessed through `barray`, according to the data matrix accessed through `bmat`.