Branch:
user/anddt/development/glm
11.0
12.0
12.1
12.2
13.0
13.1
13.37
14.0
14.1
14.2
15.0
bedlam
bedlam-name-fixes
dive
erik
gitignore
libressl-gopher-test
master
misc-fixes
python-renames
rworkman
urchlay
user/aclemons/updates
user/anddt/development/acpica
user/anddt/development/glm
user/anddt/development/gnustep-base
user/anddt/development/gnustep-make
user/anddt/games/assaultcube-reloaded
user/anddt/games/doomseeker
user/anddt/games/prboom-plus
user/anddt/games/rocksndiamonds
user/anddt/games/rottexpr
user/anddt/games/srb2
user/anddt/graphics/blender
user/anddt/graphics/maim
user/anddt/ham/chirp
user/anddt/ham/hamlib
user/anddt/libraries/girara
user/anddt/libraries/goffice
user/anddt/libraries/gtksourceview4
user/anddt/libraries/imlib2
user/anddt/libraries/jsoncpp
user/anddt/libraries/libnova
user/anddt/libraries/libopenmpt
user/anddt/libraries/libtorrent
user/anddt/libraries/wxGTK3
user/anddt/libraries/xmlrpc-c
user/anddt/misc/discount
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user/anddt/network/putty
user/anddt/network/rclone
user/anddt/network/rtorrent
user/anddt/network/sshguard
user/anddt/network/strongswan
user/anddt/network/umurmur
user/anddt/network/yt-dlp
user/anddt/network/znc
user/anddt/office/gnumeric
user/anddt/office/sigil
user/anddt/system/FontAwesome
user/anddt/system/conky
user/anddt/system/fakeroot
user/anddt/system/hplip-plugin
user/anddt/system/postgresql
user/anddt/system/testdisk
user/anddt/system/worker
user/anddt/system/xen
user/anddt/system/zzzfm
user/belka/updates
user/chris.willing/updates
user/dslackw/updates
user/elyk/updates
user/kingbeowulf/updates
user/mario/updates
user/ponce/updates
user/pprkut/updates
willysr
wxWidgets-wip
GPG-KEY
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Matteo Bernardini
e6f72d7699
academic/seaview: Removed the treerecs dependency (ftb).
|
2 years ago | |
|---|---|---|
| .. | ||
| README | e6f72d7699 academic/seaview: Removed the treerecs dependency (ftb). | 2 years ago |
| References | 988aacfea1 academic/seaview: Added (sequence alignment and phylogeny GUI) | 12 years ago |
| doinst.sh | 988aacfea1 academic/seaview: Added (sequence alignment and phylogeny GUI) | 12 years ago |
| seaview.SlackBuild | 63daf9f79a All: Support $PRINT_PACKAGE_NAME env var | 2 years ago |
| seaview.desktop | d74ce3a23f academic/seaview: Updated for version 4.3.2. | 12 years ago |
| seaview.info | e6f72d7699 academic/seaview: Removed the treerecs dependency (ftb). | 2 years ago |
| slack-desc | 8a6006c3b9 academic/seaview: Updated for version 4.6.3. | 6 years ago |
README
SeaView is a multiplatform, graphical user interface for multiple
sequence alignment and molecular phylogeny. Features:
- Reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA,
PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic
trees.
- Drives programs muscle or Clustal Omega for multiple sequence
alignment, and also allows to use any external alignment
algorithm able to read and write FASTA-formatted files.
- Drives the Gblocks program to select blocks of evolutionarily
conserved sites.
- Computes phylogenetic trees by parsimony, using PHYLIP's dnapars /
protpars algorithm, distance, with NJ or BioNJ algorithms on a variety
of evolutionary distances, maximum likelihood, driving program PhyML
- Can use the Transfer Bootstrap Expectation method to compute the
bootstrap support of PhyML and distance trees.
- Prints and draws phylogenetic trees on screen, SVG, PDF or PostScript
files.
- Allows to download sequences from EMBL / GenBank / UniProt.
For details and citation:
Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a
multiplatform graphical user interface for sequence alignment and
phylogenetic tree building. Molecular Biology and Evolution
27(2):221-224.
sequence alignment and molecular phylogeny. Features:
- Reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA,
PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic
trees.
- Drives programs muscle or Clustal Omega for multiple sequence
alignment, and also allows to use any external alignment
algorithm able to read and write FASTA-formatted files.
- Drives the Gblocks program to select blocks of evolutionarily
conserved sites.
- Computes phylogenetic trees by parsimony, using PHYLIP's dnapars /
protpars algorithm, distance, with NJ or BioNJ algorithms on a variety
of evolutionary distances, maximum likelihood, driving program PhyML
- Can use the Transfer Bootstrap Expectation method to compute the
bootstrap support of PhyML and distance trees.
- Prints and draws phylogenetic trees on screen, SVG, PDF or PostScript
files.
- Allows to download sequences from EMBL / GenBank / UniProt.
For details and citation:
Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a
multiplatform graphical user interface for sequence alignment and
phylogenetic tree building. Molecular Biology and Evolution
27(2):221-224.