| Feature |
Added |
UBLASTX
translated local search (nucleotide query, amino acid database).
|
3.0.627 |
Support
for --blastout in UBLAST[X].
|
3.0.627 |
UBLAST
algorithm for local search.
|
3.0 |
E-values
reported for local and global alignments (--uc_evalue and --evalue
options).
|
3.0 |
Support
for different definitions of identity (--iddef option).
|
3.0 |
--maxtargets
T option to terminate search after examining T targets.
|
3.0 |
More
intuitive database search command-line: --query and --db options as
alternatives to --input and --lib, imply --libonly.
|
2.1 |
Hierarchical clustering
(--uhire).
|
2.1 |
Chimeric sequence detection
(--uchime).
|
2.1 |
"Clumping":
clustering with the goal of finding clusters of a given size. Useful
for dividing data into subsets tractable for further analysis (--uhire
with --clumpfasta).
|
2.1 |
Support
for construction of very large, high-quality multiple alignments (--mergeclumps).
|
2.1 |
--fastapairs filename option added. Writes all pair-wise
alignments of queries to target sequences in FASTA format. Much easier
for scripts to parse than the --blastout format, and more robust
against future changes.
|
1.1.579 |
| Bug |
First |
Fixed |
Segfault
if star ('*') character in amino acid sequence in database or input.
|
1.0 |
3.0.627 |
| Native
Mac text file format not supported for FASTA in some cases. Symptom is
this message: "---Fatal error--- sfasta.cpp(80) assert failed:
ptr != 0". Work-around is to translate the file to Unix format,
which you can do with this command:
tr "\015" "\n" <
Mac.fasta > Linux.fasta
|
1.0 |
Open |
Segfault
may occur when attempting de novo clustering if more than 100,000
clusters are found.
|
1.0 |
3.0.623 |
Some pre-built binaries would
segfault at apparently random times.
|
1.1.570 |
1.1.574 |
Non-intel processor compile
error.
|
1.1.570 |
1.1.574 |
Severe bug in--nowordcountfilter causes slow speed,
reduced sensitivity.
|
1.1.570 |
1.1.579 |
HSPs not found if query sequence and
target sequence not in same case.
|
1.1.570 |
2.1.15 |
Error in 32-bit builds reading file
> 2 Gb.
|
1.1.570 |
2.1.15 |
FASTA files containing CR bytes, e.g.
DOS text format, can cause various problems that are not always
obvious or visible at all without careful analysis -- uclust may give
the wrong answer without crashing. Work-around is to convert to Unix text format
using a utility like dos2unix.
|
1.1.570 |
2.1.600 |
--uc2fasta doesn't work correctly if lower-case letters
in input, causes --ustar to crash.
|
1.0 |
1.1.579 |
--staralign
fails if --rev was used in the searching or clustering step.
|
1.0 |
Open |
Crash if FASTA label contains
'>'.
|
1.0 |
Open |
--clstr2uc
fails with segfault (Linux) or silent exit (Windows).
|
1.0 |
4.0 |