Biology Reference
In-Depth Information
4 Notes
1. By default, Clustal Omega uses the MAC algorithm to align
profiles. This algorithm requires a certain amount of memory.
If this amount of memory is not available, then Clustal Omega
switches to the Viterbi algorithm. However, it is not straight-
forward to establish the amount of RAM available on different
machines running different operating systems. Clustal Omega
therefore assumes that it will have 2 GB
2,048 MB of mem-
ory available for the MAC alignment. Should one be fortunate
enough to have more than 2 GB of RAM then this can be
communicated by setting the --MAC-RAM flag to the appro-
priate size (in MB). For example, on a machine with 4 GB of
RAM one might specify:
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$ clustalo -i globin.fa --MAC-RAM
4096
¼
1,024 MB). In reality
one might want to reduce the --MAC-RAM value, to allow for
memory usage other than the MAC alignment.
2. The “configure” shell script attempts to guess correct values for
various system-dependent variables used during compilation.
It uses those values to create a “Makefile” in each directory of
the package. It may also create one or more “.h” files contain-
ing system-dependent definitions. Finally, it creates a shell
script “config.status” that one can run in the future to recreate
the current configuration, and a file “config.log” containing
compiler output (useful mainly for debugging “configure”).
3. Clustal Omega needs argtable2 (
http://argtable.sourceforge.
one may have to point configure to its installation directory.
For example, if on a Mac with argtable installed via MacPorts
then one should use the following command line:
where 4096 corresponds to 4 GB (
4
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$./configureCFLAGS
'-I/opt/local/include'
LDF
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'-L/opt/local/lib'
4. Clustal Omega will automatically support multi-threading if
the compiler supports OpenMP. For some reason automake's
OpenMP detection for Apple's gcc is broken. OpenMP detec-
tion can be forced by calling configure as follows:
LAGS
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$./configure OPENMP_CFLAGS
'-fopenmp' CFLAGS
'-
DHAVE_OPENMP'
5. Distance matrix output can be initiated by specifying --distmat-
out. However, this is not possible in default (mBed) mode
because mBed does not calculate a full distance matrix. There-
fore one must specify full distance matrix calculation by setting
--full. For example
