Installing External Dependencies

PASV relies on a few other software packages to align sequences.

Currently, PASV supports Clustal Omega, MAAFT, or HMMER.

For detailed instructions on installing these packages, please consult their respective installation pages.

Example installation instructions

Here are some basic instructions for installing the required software on the latest versions of MacOS and Ubuntu Linux.

Note: These instructions are taken from one of the GitHub actions that builds and tests PASV, so if it is passing then these instructions should still work if you have a similar OS.

Clustal Omega (Linux)

mkdir -p $HOME/.local/bin
CLUSTALO_EXE=$HOME/.local/bin/clustalo
\curl -L http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 > "$CLUSTALO_EXE"
chmod 755 "$CLUSTALO_EXE"

Clustal Omega (Mac)

Note that Clustal Omega 1.2.4 is not available on MacOS.

mkdir -p $HOME/.local/bin
CLUSTALO_EXE=$HOME/.local/bin/clustalo
\curl -L http://www.clustal.org/omega/clustal-omega-1.2.3-macosx > "$CLUSTALO_EXE"
chmod 755 "$CLUSTALO_EXE"

MAFFT

\curl -L https://mafft.cbrc.jp/alignment/software/mafft-7.481-without-extensions-src.tgz \
  | tar xz
cd mafft-*/core/ && make clean && make && sudo make install

HMMER

\curl -L http://eddylab.org/software/hmmer/hmmer-3.3.2.tar.gz | tar xz
cd hmmer-3.3.2 && ./configure && make && sudo make install