Distance matrix file
A distance matrix file contains pair-wise distances
between a set of sequences.
A distance is specified as a
fractional identity (the default) or a fractional difference which is 1.0 -
(fractional identity). Fractional identity is more familiar to most people and
more consistent with other USEARCH commands, but fractional difference behaves
as a distance measure because it increases with distance (it is zero for
identical sequences and one for maximally different sequences). To specify
fractional difference, use the -distmo option (for
an output file) or -distmi option (for an input
It is straightforward to add support for other measures of
if this would be useful for your applications,
let me know.
USEARCH distance matrices are usually "sparse", meaning
that only a subset is calculated. Pairs with low identities (determined by a
threshold and/or by word-counting heuristics) are omitted from the matrix, which
can dramatically reduce the time and space required to compute and store a
matrix for large sequence sets.
Four formats are supported for distance matrices:
tabbed_pairs, square, phylip_square and phylip_lower_triangular. In formats that
require all distances to be included (all except tabbed_pairs), unknown values
are given as 0.0 (identity) or 1.0 (distance).
The matrix is stored as a tabbed text file. There are three fields in each
line: Label1, Label2 and Distance. Pairs with distances that are unknown or
below the threshold are omitted to save disk space. To simplify sequential
parsing of this format, the file always starts with the diagonal, i.e. one line
for each sequence giving a distance of zero from itself, e.g. Label1 Label1 1.0
(identity) or Label1 Label1 0.0 (difference). This ensures that the labels of
all sequences are known before any off-diagonal entries are processed.
The matrix is stored as a tabbed text file. There is one header line,
followed by one line per sequence. The header line starts with an integer giving
the number of sequences, followed by a tab-separated list of sequence labels.
The following lines start with a sequence label, followed by a tab-separated
list of distances. This format may become large, and hard to read by humans,
when there are many sequences.
phylip_square and phylip_lower_triangular formats
These formats are compatible with Phylip, see
Phylip documentation for format details. You should use -distmo
fractdiff (fractional difference) if you are going to use Phylip to process a
distance matrix generated by USEARCH because Phylip assumes a distance metric
where zero means identical sequences and increasing values indicate decreasing