|
Option |
|
Description |
|
‑alnout |
|
Human-readable
alignments. |
|
‑userout |
|
Tab-separated text file, fields are
specified by -userfields. |
|
‑uc |
|
Tab-separated text file with records for
hits and clusters. |
|
‑fastapairs |
|
FASTA file. Each pair of sequences is a
hit with the query first then the target, with gaps inserted to
align them. |
|
‑centroids |
|
FASTA file for centroid
sequences. |
|
‑consout |
|
FASTA file for consensus
sequences. |
|
‑blast6out |
|
Tab-separated text file compatible with
the NCBI BLAST m8 and outfmt 6
formats. |
|
-matched |
|
FASTA file containing
query sequences that matched the database. Supported by v6.0.229 and later. |
|
-notmatched |
|
FASTA file containing
query sequences that did not match the database. Supported by v6.0.229 and
later. |
|
-dbmatched |
|
FASTA file containing
database sequences matched to at least one query sequence. Supported by v6.0.229 and later.
If -sizeout is specified, the number of queries that matched this sequence is
written as a size annotation. |
|
-dbnotmatched |
|
FASTA file containing
database sequences that were not matched to a query sequence. Supported by v6.0.229 and
later. |
|
-msaout |
|
FASTA file containing
a multiple alignment of each cluster. Supported by v6.0.307 and later. |