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20 hours ago •
etetoolkit
etetoolkit
please provide list external tools with expected version
Hello,
I'm trying to dig the etee external tools dependencies.
and found some conflicting informations.
meta.yaml extracted from https://anaconda.org/etetoolkit/ete_toolchain/3.0.0/download/linux-64/ete_toolchain-3.0.0-h73706c9_0.tar.bz2
gives the following list for externale tools (NB I removed system components)
- phylobayes 4.1c.*
- phyml 20160115.patched.*
- muscle 3.8.31.*
- kalign 2.03.*
- slr 1.4.3.*
- iqtree 1.5.5.*
- pmodeltest 1.4.*
- trimal 1.4.*
- argtable2 2.13.*
- t_coffee 11.00.*
- raxml 8.2.11.*
- dialigntx 1.0.2.*
- clustalo 1.2.4.*
- paml 4.8.*
- mafft 6.861.*
- fasttree 2.1.*
ete3/tools/ete_build_lib/apps.py gives following information
APPTYPES = {
"aligners": set(["muscle", "mafft", "clustalo", "metaligner", "dialingtx", "tcoffee"]),
"model testers": set(["prottest", "pmodeltest"]),
"alg cleaners": set(["trimal"]),
"tree builders": set(["fasttree", "phyml", "raxml", "iqtree"]),
"COG selectors": set(["cogselector"]),
"alg concatenators": set(["concatalg"]),
}
and https://github.com/etetoolkit/ext_apps/tree/master/src list
<html xmlns:v="urn:schemas-microsoft-com:vml"
xmlns:o="urn:schemas-microsoft-com:office:office"
xmlns:x="urn:schemas-microsoft-com:office:excel"
xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta name=ProgId content=Excel.Sheet>
<meta name=Generator content="Microsoft Excel 15">
<link id=Main-File rel=Main-File
href="file:////Users/edeveaud/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip.htm">
<link rel=File-List
href="file:////Users/edeveaud/Library/Group%20Containers/UBF8T346G9.Office/TemporaryItems/msohtmlclip/clip_filelist.xml">
<style>
<!--table
{mso-displayed-decimal-separator:"\,";
mso-displayed-thousand-separator:" ";}
@page
{margin:.75in .7in .75in .7in;
mso-header-margin:.3in;
mso-footer-margin:.3in;}
tr
{mso-height-source:auto;}
col
{mso-width-source:auto;}
br
{mso-data-placement:same-cell;}
td
{padding-top:1px;
padding-right:1px;
padding-left:1px;
mso-ignore:padding;
color:black;
font-size:12.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Calibri, sans-serif;
mso-font-charset:0;
mso-number-format:General;
text-align:general;
vertical-align:bottom;
border:none;
mso-background-source:auto;
mso-pattern:auto;
mso-protection:locked visible;
white-space:nowrap;
mso-rotate:0;}
.xl64
{font-size:14.0pt;
font-family:menlo, sans-serif;
mso-font-charset:0;}
.xl65
{color:#0563C1;
text-decoration:underline;
text-underline-style:single;}
-->
</style>
</head>
<body link="#0563C1" vlink="#954F72">
--
phylobayes4.1c
phyml-20120412-patched
muscle3.8.31
kalign-2.03
iqtree-omp-1.4.2-Linux // iqtree-omp-1.4.2-MacOSX
trimal-1.4
T-COFFEE_distribution_Version_11.00.8cbe486
standard-RAxML-8.2.8
DIALIGN-TX_1.0.2
clustal-omega-1.2.1
mafft-6.861-without-extensions
FastTree2
pmodeltest
prank-100802
probcons-1.12
paml4.8
slr
argtable2-13
consel
treebest
can you provide a comprehensive list of dependencies with version and upstream url ?
regards
Eric
