[med-svn] [Git][med-team/terraphast][master] 8 commits: debian/tests: add a test using the real-world Meusemann insect phylogenomics...
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Oct 17 19:54:28 BST 2026
Andreas Tille pushed to branch master at Debian Med / terraphast
Commits:
818baa7f by Andreas Tille at 2026-10-17T20:00:31+02:00
debian/tests: add a test using the real-world Meusemann insect phylogenomics dataset (bundled in debian/tests/data, with origin documented in debian/tests/README)
- - - - -
9f38ba36 by Andreas Tille at 2026-10-17T20:48:09+02:00
No need for dh-exec
- - - - -
9b91dfd2 by Andreas Tille at 2026-10-17T19:48:17+01:00
Reformat the Last-Update date as ISO YYYY-MM-DD.
Changes-By: lintian-brush
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/dynamic_lib.patch]
See-also: https://lintian.debian.org/tags/invalid-dep3-format-patch-wrong-last-update.html
- - - - -
2c3b3c10 by Andreas Tille at 2026-10-17T19:48:17+01:00
Remove redundant Priority: optional from source stanza.
Changes-By: lintian-brush
Fixes: lintian: source: redundant-priority-optional-field
See-also: https://lintian.debian.org/tags/redundant-priority-optional-field.html
- - - - -
8c9f1531 by Andreas Tille at 2026-10-17T19:48:17+01:00
Update standards version to 4.7.4, no changes needed.
Upgrade checklist verified:
4.7.3 → 4.7.4:
* Package is not in non-free-firmware
Changes-By: lintian-brush
Fixes: lintian: source: out-of-date-standards-version 4.7.2 (released 2025-02-27) (current is 4.7.4.1)
See-also: https://lintian.debian.org/tags/out-of-date-standards-version.html
- - - - -
261be40c by Andreas Tille at 2026-10-17T19:48:19+01:00
Set upstream metadata fields: Bug-Database, Repository.
Changes-By: lintian-brush
Fixes: lintian: source: upstream-metadata-missing-repository [debian/upstream/metadata]
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
eba28bb9 by Andreas Tille at 2026-10-17T20:49:20+02:00
cme fix dpkg-control
- - - - -
c5db3e8b by Andreas Tille at 2026-10-17T20:51:17+02:00
Upload to unstable
- - - - -
11 changed files:
- debian/changelog
- debian/control
- debian/libterraces-dev.install
- debian/libterraces0.install
- debian/patches/dynamic_lib.patch
- + debian/terraphast.examples
- + debian/tests/README
- + debian/tests/data/Meusemann.data
- + debian/tests/data/Meusemann.nwk
- debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-terraphast (0.1.0+dfsg-2) UNRELEASED; urgency=medium
+terraphast (0.1.0+dfsg-2) unstable; urgency=medium
* Fix heap corruption when the multitree memory limit is reached
(Closes: #1139550)
@@ -7,8 +7,17 @@ terraphast (0.1.0+dfsg-2) UNRELEASED; urgency=medium
sites lacking any occurrence, aborting validated_run
* debian/tests: fix run-unit-test autopkgtest; generate test data with
the installed tools instead of referencing non-installed examples
-
- -- Andreas Tille <tille at debian.org> Sat, 17 Oct 2026 00:00:00 +0200
+ * debian/tests: add a test using the real-world Meusemann insect
+ phylogenomics dataset (bundled in debian/tests/data, with origin
+ documented in debian/tests/README)
+ * No need for dh-exec
+ * Reformat the Last-Update date as ISO YYYY-MM-DD.
+ * Remove redundant Priority: optional from source stanza.
+ * Update standards version to 4.7.4, no changes needed.
+ * Set upstream metadata fields: Bug-Database, Repository.
+ * cme fix dpkg-control
+
+ -- Andreas Tille <tille at debian.org> Sat, 17 Oct 2026 20:49:25 +0200
terraphast (0.1.0+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,16 +1,14 @@
Source: terraphast
-Standards-Version: 4.7.2
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders:
Andreas Tille <tille at debian.org>,
Section: science
-Priority: optional
Build-Depends:
- debhelper-compat (= 13),
+ debhelper-compat (= 14),
+ catch,
cmake,
d-shlibs,
- dh-exec,
- catch,
libgmp3-dev,
Vcs-Browser: https://salsa.debian.org/med-team/terraphast
Vcs-Git: https://salsa.debian.org/med-team/terraphast.git
@@ -21,9 +19,9 @@ Package: terraphast
Architecture: any
Section: libs
Depends:
- ${shlibs:Depends},
- ${misc:Depends},
libterraces0 (= ${binary:Version}),
+ ${misc:Depends},
+ ${shlibs:Depends},
Description: enumerate terraces in phylogenetic tree space
Terraphast takes a .nkw file in Newick format and a genes/sites file,
which denotes whether (1) or not (0) gene i is present in species j.
@@ -36,8 +34,8 @@ Package: libterraces0
Architecture: any
Section: libs
Depends:
- ${shlibs:Depends},
${misc:Depends},
+ ${shlibs:Depends},
Description: enumerate terraces in phylogenetic tree space (shared lib)
Terraphast takes a .nkw file in Newick format and a genes/sites file,
which denotes whether (1) or not (0) gene i is present in species j.
@@ -53,8 +51,8 @@ Architecture: any
Section: libdevel
Depends:
libterraces0 (= ${binary:Version}),
- ${shlibs:Depends},
${misc:Depends},
+ ${shlibs:Depends},
Description: enumerate terraces in phylogenetic tree space (development lib)
Terraphast takes a .nkw file in Newick format and a genes/sites file,
which denotes whether (1) or not (0) gene i is present in species j.
=====================================
debian/libterraces-dev.install
=====================================
@@ -1,3 +1,2 @@
-#!/usr/bin/dh-exec
obj-*/*_c.a usr/lib/${DEB_HOST_MULTIARCH}/
obj-*/*_c.so usr/lib/${DEB_HOST_MULTIARCH}/
=====================================
debian/libterraces0.install
=====================================
@@ -1,2 +1 @@
-#!/usr/bin/dh-exec
obj-*/*_c.so.* usr/lib/${DEB_HOST_MULTIARCH}/
=====================================
debian/patches/dynamic_lib.patch
=====================================
@@ -1,6 +1,6 @@
Author: Andreas Tille <tille at debian.org>,
Aaron M. Ucko <ucko at debian.org>
-Last-Update: Wed, 20 Oct 2021 09:51:23 +0200
+Last-Update: 2021-10-20
Description: Attempt to create shared library
This patch is deactivated since the build fails with it.
Thus we simply stick to the existing static library
=====================================
debian/terraphast.examples
=====================================
@@ -0,0 +1 @@
+debian/tests/data/*
=====================================
debian/tests/README
=====================================
@@ -0,0 +1,32 @@
+# terraphast autopkgtest data
+
+The files in `data/` are used by the `run-unit-test` autopkgtest as a
+real-world test case.
+
+* `Meusemann.nwk` - a Newick tree (117 taxa)
+* `Meusemann.data` - an occurrence matrix (117 taxa x 97 sites)
+
+## Origin and download location
+
+Both files are the original "Meusemann" insect phylogenomics dataset as
+shipped in the terraphast upstream repository:
+
+* Repository: https://github.com/terraphast/terraphast
+* Directory: data/original/
+
+Download URLs:
+
+* https://raw.githubusercontent.com/terraphast/terraphast/master/data/original/Meusemann.nwk
+* https://raw.githubusercontent.com/terraphast/terraphast/master/data/original/Meusemann.data
+
+SHA-256 checksums (verified against the upstream files):
+
+* Meusemann.nwk `8128ef64746ae85487758d7d44f18d41bec1b51e2f9d145caacb60980276a1ee`
+* Meusemann.data `07d0bfbf5e7ebb8df34d4e22dc147885342831bfed70ca8b96c2c6c73b28cef9`
+
+## Underlying biological dataset
+
+Meusemann K, von Reumont BM, Simon S, Roeding F, Strauss S, Kueck P,
+Ebersberger I, Walzl M, Pass G, Breuers S, et al. (2010).
+"A phylogenomic approach to resolve the arthropod tree of life."
+Molecular Biology and Evolution 27(11):2451-2464.
=====================================
debian/tests/data/Meusemann.data
=====================================
@@ -0,0 +1,118 @@
+117 97
+1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 0 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 0 0 0 1 0 0 1 0 1 1 1 1 0 1 1 1 0 1 0 1 1 1 0 1 0 0 1 1 0 0 1 1 1 1 1 1 Acanthoscurria_gomesiana
+1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 0 1 0 0 0 0 1 0 1 0 1 1 0 0 0 1 0 0 1 1 1 0 0 1 0 1 1 1 0 1 0 0 1 1 1 0 0 0 1 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 1 0 0 0 0 0 Acerentomon_franzi
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 0 0 0 1 1 0 1 1 1 1 1 0 1 0 1 0 1 1 1 Acyrthosiphon_pisum
+0 0 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 0 1 Aedes_aegypti
+0 1 1 1 0 1 0 1 1 1 1 0 0 1 1 1 1 1 0 0 1 1 1 0 1 0 1 0 0 0 0 0 1 1 0 1 1 1 0 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 1 1 1 0 1 1 1 0 0 0 1 1 0 1 0 1 0 0 0 1 0 0 0 1 0 0 0 1 0 Amblyomma_americanum
+1 1 0 0 1 1 1 0 0 1 1 0 0 0 1 1 0 0 1 1 0 1 0 1 1 0 0 0 1 1 0 1 1 0 0 1 0 1 1 1 1 0 1 0 1 0 0 0 1 0 0 0 0 1 1 1 0 1 1 0 1 0 0 1 0 1 0 1 1 0 1 0 1 0 0 0 0 0 0 1 1 0 1 1 0 1 1 1 1 0 0 1 0 0 1 0 1 Amblyomma_variegatum
+0 0 1 1 0 1 0 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 0 1 0 1 1 1 0 0 0 0 1 0 0 0 1 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 1 0 1 0 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 1 0 Anopheles_albimanus
+1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 Anopheles_gambiae
+1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 0 0 0 0 1 1 1 1 1 1 0 0 0 1 1 0 0 1 1 1 0 1 0 0 1 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 Anoplodactylus_eroticus
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 1 1 0 0 0 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 1 1 0 1 1 Antheraea_assama
+1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 0 1 0 0 0 1 1 0 0 0 1 1 0 1 1 0 0 1 0 1 0 1 0 0 0 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 1 0 0 0 0 0 1 0 1 1 1 0 0 1 0 0 0 1 1 Antheraea_mylitta
+1 0 0 0 1 1 0 0 1 0 1 0 1 1 1 1 1 1 1 0 1 0 0 0 1 0 1 0 0 1 0 0 1 1 0 1 1 0 1 1 0 1 0 0 0 0 1 0 0 0 1 1 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 1 0 0 1 0 0 1 0 1 1 1 0 0 0 1 1 0 0 0 1 0 0 Anurida_maritima
+0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 0 1 1 0 0 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 0 1 0 0 1 1 1 0 1 1 0 1 0 1 1 1 0 1 1 1 0 0 1 1 0 1 0 0 1 1 1 1 0 Aphis_gossypii
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Apis_mellifera
+1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 0 1 0 0 1 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 0 0 1 0 1 1 0 0 1 0 1 1 1 1 1 0 0 0 1 0 0 0 0 1 0 1 0 1 0 0 0 1 0 Archispirostreptus_gigas
+1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 1 0 0 0 1 1 0 1 0 1 1 1 0 1 0 0 1 1 1 0 0 0 0 0 1 0 1 0 0 0 1 0 1 1 0 0 1 0 1 1 0 0 1 0 0 0 1 0 0 0 0 1 1 0 0 1 0 0 0 1 0 Argopecten_irradians
+1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 1 0 0 1 1 1 1 0 0 1 1 0 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 0 0 0 1 1 1 0 Armigeres_subalbatus
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 0 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 1 1 Artemia_franciscana
+1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 0 0 0 1 1 1 1 0 0 1 0 1 1 1 0 0 0 1 0 0 0 0 0 1 0 1 1 0 0 1 1 1 1 0 0 0 1 0 0 1 0 0 0 0 1 1 1 1 Ascaris_suum
+1 0 1 1 0 0 1 0 0 0 0 1 1 0 1 0 0 1 0 0 1 0 1 0 0 1 1 1 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1 0 1 1 1 1 0 0 0 1 0 1 0 0 1 0 1 0 0 1 0 0 1 0 0 1 0 0 0 1 1 1 1 1 1 1 0 0 0 1 0 0 1 0 1 0 1 1 0 0 1 0 0 1 Baetis_sp.
+1 0 0 1 1 1 0 1 0 0 1 1 1 0 0 1 1 1 0 1 1 0 1 0 0 1 1 1 0 0 1 0 0 0 1 0 1 1 1 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 1 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 Bemisia_tabaci
+1 0 1 1 0 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 0 1 0 1 1 1 0 1 0 0 0 1 1 1 1 1 0 0 0 1 0 1 0 1 1 0 0 0 1 1 0 1 1 0 0 0 0 1 1 0 1 0 1 1 1 1 1 0 0 0 1 0 0 1 1 0 1 0 0 0 1 0 1 0 1 0 Bicyclus_anynana
+1 1 0 0 0 0 1 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 1 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 1 0 1 0 1 1 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 1 1 0 1 0 1 0 1 0 0 0 0 1 0 0 Blattella_germanica
+1 1 1 1 0 1 0 0 0 1 0 0 0 0 1 0 1 0 0 1 0 0 0 1 0 1 0 0 0 1 0 1 1 0 0 1 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 1 1 Blomia_tropicalis
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Bombyx_mori
+1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Boophilus_microplus
+1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 Caenorhabditis_briggsae
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 Caenorhabditis_elegans
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 Caenorhabditis_remanei
+1 1 1 0 0 1 1 0 0 1 1 0 0 0 1 0 0 0 1 1 0 0 0 1 0 0 0 0 1 0 1 0 1 0 0 0 0 1 1 1 0 0 1 1 1 0 0 0 1 0 0 1 0 0 0 1 0 0 1 0 0 0 0 1 1 0 1 1 1 1 1 0 0 0 0 1 0 1 1 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 1 Calanus_finmarchicus
+1 1 0 1 0 1 1 0 0 1 1 1 1 0 1 1 1 0 0 1 0 1 1 1 1 0 0 0 1 1 0 1 1 1 0 0 1 1 1 0 0 1 0 0 0 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 1 0 0 1 1 1 0 0 0 0 1 1 0 1 0 0 0 1 0 0 0 1 1 0 0 0 0 Callinectes_sapidus
+1 1 0 1 1 1 1 0 1 1 1 0 0 0 1 1 1 1 0 1 1 1 1 1 0 1 0 0 1 1 0 1 1 0 0 0 1 1 0 1 0 1 0 1 1 1 0 1 0 1 1 1 1 0 1 1 1 0 1 0 1 1 0 0 1 0 0 1 1 1 1 1 0 1 1 0 1 0 1 0 0 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 1 Campodea_cf_fragilis
+0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 Capitella_capitata
+1 1 0 1 1 1 0 0 0 1 1 0 1 0 1 1 1 0 1 1 1 0 0 1 1 0 0 0 1 1 0 1 1 0 0 1 0 1 1 1 0 0 1 1 1 1 0 0 1 0 0 1 0 1 1 1 1 0 1 1 1 0 0 0 0 1 1 1 1 1 0 1 1 0 0 1 0 1 1 0 1 0 1 0 1 0 1 1 1 1 0 1 1 0 0 0 1 Carcinus_maenas
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 1 Ceratitis_capitata
+1 1 0 1 0 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 1 0 1 1 1 1 1 1 Chironomus_tentans
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 0 1 1 0 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 1 1 1 0 1 0 1 1 Crassostrea_gigas
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Culex_pipiens_quinquefasciatus
+1 0 1 1 1 1 0 1 1 0 0 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 0 1 0 1 1 0 1 1 1 1 0 0 1 0 1 0 0 1 1 0 1 0 1 0 0 1 1 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 1 0 0 0 1 1 0 0 0 1 0 0 1 0 0 0 0 1 0 1 0 1 1 0 0 1 0 Culicoides_sonorensis
+1 1 1 1 1 1 1 0 1 1 1 0 0 0 1 1 1 0 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 Danaus_plexippus
+1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 1 0 1 1 1 0 1 1 1 1 1 1 1 1 0 0 1 1 1 0 1 1 0 0 0 0 1 1 0 0 0 1 1 1 0 0 0 0 0 1 1 1 0 0 0 1 1 1 0 0 1 1 0 1 0 Daphnia_magna
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Daphnia_pulex
+0 0 1 0 0 1 0 1 1 1 0 1 1 1 0 1 0 1 0 1 1 0 0 0 1 0 1 1 0 0 0 0 0 1 1 1 1 0 0 1 0 1 0 0 0 1 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1 0 0 0 1 1 Dermacentor_andersoni
+1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 0 1 1 0 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 Diabrotica_virgifera_virgifera
+1 1 1 1 1 1 1 0 0 1 1 1 0 0 1 1 1 0 0 0 1 1 1 1 1 1 0 1 0 0 0 1 1 0 1 0 1 1 0 1 1 1 0 0 0 1 1 0 0 0 0 0 1 0 0 1 1 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 1 0 1 0 0 0 0 0 Diaprepes_abbreviatus
+1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 0 1 1 1 0 0 1 1 1 0 1 1 1 1 Drosophila_ananassae
+0 1 1 1 0 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 0 1 1 0 1 1 1 0 0 1 1 1 0 0 0 1 1 0 0 1 0 0 1 1 0 0 1 1 0 0 1 0 1 1 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 0 0 1 0 1 0 Drosophila_arizonae
+1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 Drosophila_erecta
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Drosophila_melanogaster
+1 1 1 1 1 1 1 1 0 1 1 0 1 0 1 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 0 1 0 1 1 1 0 1 0 1 1 1 1 1 0 0 0 0 1 1 0 0 1 0 1 0 0 1 1 0 1 1 0 1 1 0 1 0 1 0 0 1 1 0 1 1 0 0 0 1 0 1 1 0 0 0 1 1 0 0 0 1 0 0 Endeis_spinosa
+1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 0 1 1 0 0 1 1 0 1 1 0 1 1 1 1 0 0 1 1 1 1 0 0 1 0 0 0 0 1 1 0 1 1 0 1 0 0 1 0 1 0 1 1 0 1 1 0 0 1 1 0 1 0 1 1 1 0 Epiphyas_postvittana
+0 1 1 1 0 1 0 0 1 1 1 1 1 1 1 0 0 1 1 1 1 0 1 0 1 1 1 0 0 1 0 0 1 0 1 1 1 1 1 1 0 0 0 0 0 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 1 0 1 0 1 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 1 0 Euperipatoides_kanangrensis
+1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 0 1 1 1 0 0 1 0 0 1 1 1 1 0 1 0 1 0 0 0 1 1 0 1 1 1 0 0 0 0 1 1 0 0 0 0 0 1 1 0 1 0 0 1 0 0 Fenneropenaeus_chinensis
+0 1 1 1 0 0 0 1 1 0 0 1 0 1 0 0 0 1 1 0 0 1 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 1 0 0 1 0 1 0 0 1 0 1 0 0 1 0 1 1 0 0 0 0 0 0 1 1 1 1 0 0 0 1 0 0 1 0 0 0 1 1 0 0 1 0 0 1 1 0 0 Folsomia_candida
+1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 0 0 1 1 0 1 0 0 0 1 1 1 1 1 1 0 0 1 0 1 1 0 0 0 1 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0 0 1 1 0 0 0 0 1 1 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 1 0 1 1 1 Gammarus_pulex
+1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Glossina_morsitans_morsitans
+1 0 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 0 0 1 1 1 1 0 1 1 1 1 1 0 0 0 0 0 1 1 1 1 1 1 0 1 0 0 1 1 1 0 1 0 1 0 0 1 0 0 1 0 0 0 1 0 1 1 0 1 0 0 1 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 Glycyphagus_domesticus
+1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 0 1 0 1 0 0 1 1 0 1 1 0 0 0 0 0 0 1 1 0 0 1 0 0 1 1 0 1 0 0 0 0 0 0 1 0 0 0 1 1 1 0 1 1 1 1 1 0 1 0 1 1 1 1 0 0 0 1 0 1 0 0 0 0 1 1 0 1 0 Graphocephala_atropunctata
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 0 1 1 0 1 1 1 1 0 1 1 1 1 1 1 1 0 0 1 1 0 1 1 0 0 1 0 1 1 1 1 1 0 0 0 0 1 1 0 0 1 1 1 0 1 1 0 0 1 0 1 1 1 0 1 1 1 1 0 1 1 0 0 1 1 1 Gryllus_bimaculatus
+1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 1 1 1 1 0 1 0 0 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 0 1 1 0 1 0 0 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 0 1 0 1 1 1 1 Haemonchus_contortus
+1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 0 1 1 0 0 1 1 0 1 0 1 1 1 1 0 1 1 0 0 0 0 0 1 1 0 1 1 1 Heliconius_erato
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 0 0 1 1 1 0 1 1 0 1 0 1 1 1 0 1 1 1 0 1 0 1 1 1 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 1 0 0 1 1 1 0 1 0 1 1 1 0 0 0 0 0 1 0 0 1 0 1 0 1 0 Heliconius_melpomene
+1 0 0 0 1 1 1 0 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 0 1 0 1 0 0 0 1 1 1 1 0 1 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 1 1 1 1 0 0 0 1 0 1 0 1 1 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 Helicoverpa_armigera
+1 1 0 1 1 1 1 0 1 1 0 0 0 0 1 1 1 0 1 1 0 0 0 1 0 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 0 0 1 1 1 0 0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 1 1 0 1 1 0 1 0 0 1 1 1 1 1 0 1 1 1 0 0 0 1 0 0 0 1 0 1 0 0 Heliothis_virescens
+0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Helobdella_robusta
+1 1 1 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 0 0 1 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 1 1 0 1 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 1 1 0 Hodotermopsis_sjoestedti
+1 1 0 1 1 1 1 1 0 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 0 1 1 1 0 1 1 0 0 1 1 Homalodisca_coagulata
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 Homarus_americanus
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 0 1 1 1 1 1 0 1 0 1 1 0 1 1 0 0 1 1 0 0 1 0 0 1 0 0 0 1 1 0 1 1 1 1 0 0 1 0 0 0 1 0 0 0 1 1 0 0 1 0 0 1 0 1 1 Hypsibius_dujardini
+1 1 0 1 1 1 1 0 0 1 1 0 0 1 1 1 1 0 1 0 1 1 0 1 1 0 1 1 1 0 1 1 1 1 0 1 1 1 0 1 0 0 1 1 1 1 1 0 0 1 0 1 0 1 0 0 0 1 0 1 1 0 0 0 1 1 1 1 0 1 0 0 1 1 1 1 0 1 0 1 0 1 1 0 0 0 0 1 0 1 0 0 0 0 1 1 0 Ischnura_elegans
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Ixodes_scapularis
+1 1 0 1 1 1 1 0 0 1 1 0 0 0 1 1 0 0 1 1 1 1 0 1 1 0 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 1 1 1 0 0 0 0 1 1 1 0 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 0 0 1 1 0 1 0 1 0 1 1 0 1 1 1 1 1 0 1 0 1 1 0 1 Laupala_kohalensis
+1 1 1 1 1 1 1 0 0 1 1 0 1 0 1 1 1 0 1 1 1 1 0 1 1 0 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 0 0 1 0 1 1 0 0 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 1 1 0 1 0 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 0 Lepeophtheirus_salmonis
+1 1 0 1 1 1 1 0 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 0 1 1 1 0 1 1 1 1 1 1 0 0 1 1 0 1 0 0 0 1 1 1 1 0 0 1 1 0 1 0 1 0 0 1 1 1 1 0 1 1 0 0 0 0 0 1 1 1 0 0 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 Lepismachilis_y_signata
+1 1 0 1 0 1 0 0 0 1 1 0 1 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 1 1 0 1 1 0 0 0 0 1 1 1 0 0 1 0 1 0 0 0 0 0 1 0 0 1 1 1 1 0 1 0 1 0 0 0 1 1 0 0 1 0 1 1 1 0 0 1 0 0 1 0 1 0 1 0 0 0 0 0 0 1 0 1 1 0 0 1 1 Leptinotarsa_decemlineata
+1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 0 0 1 1 0 1 1 0 1 1 0 1 1 1 1 1 0 1 0 1 1 1 0 1 0 0 0 1 1 0 0 1 1 1 1 0 1 1 0 0 1 1 Limulus_polyphemus
+1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 0 1 1 1 1 1 0 0 0 0 1 0 0 0 1 1 1 0 1 0 1 1 0 0 1 0 1 1 1 1 0 1 1 0 1 0 1 0 0 0 0 1 0 1 1 0 0 1 0 0 1 0 1 0 0 0 0 0 0 1 1 0 0 0 1 1 Litopenaeus_vannamei
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 0 0 1 1 0 1 1 1 0 1 0 1 1 1 1 1 0 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 1 1 0 0 1 1 1 Locusta_migratoria
+1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 Lottia_gigantea
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 1 0 1 1 1 0 1 0 1 0 1 1 1 1 0 0 0 0 1 1 1 1 0 1 0 1 1 0 1 1 1 1 1 1 1 1 1 0 1 1 0 0 1 0 1 0 1 1 Lumbricus_rubellus
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Lutzomyia_longipalpis
+0 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 1 1 0 1 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 0 1 1 1 0 0 1 1 0 1 1 1 0 0 0 0 0 1 0 0 1 0 1 1 0 Lysiphlebus_testaceipes
+1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 0 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 0 1 1 1 1 0 0 0 0 1 1 1 1 1 0 1 0 1 1 0 1 0 1 0 1 0 1 0 1 0 1 1 0 1 0 0 0 0 0 0 1 1 0 1 1 1 1 0 0 1 0 1 1 1 1 Maconellicoccus_hirsutus
+1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 0 1 0 1 1 0 0 0 1 0 1 1 0 1 0 1 0 1 1 1 1 0 1 1 1 1 0 1 0 0 0 0 0 0 0 0 1 1 0 1 1 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 0 1 0 Manduca_sexta
+1 1 1 1 0 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 1 1 1 1 1 0 1 0 0 1 0 1 0 1 0 0 1 0 1 0 0 1 1 1 0 0 0 0 1 1 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 Marsupenaeus_japonicus
+0 0 0 1 1 1 0 1 1 0 0 1 1 1 1 1 1 1 0 1 1 1 1 1 0 0 1 1 1 1 0 1 1 0 1 1 1 0 1 1 0 1 0 0 1 1 1 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 1 0 1 0 Mayetiola_destructor
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 0 1 1 0 1 0 0 1 1 1 1 1 1 0 1 0 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 0 0 1 1 0 0 0 0 1 1 1 1 1 1 1 0 1 0 0 1 1 1 1 0 0 1 0 1 1 1 1 Meloidogyne_hapla
+1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 0 1 1 1 Myzus_persicae
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 0 1 1 1 1 1 0 0 1 1 1 1 1 0 1 1 0 1 0 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 0 Nasonia_giraulti
+1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 1 1 0 1 0 1 0 0 0 1 1 1 0 1 0 0 0 1 1 1 0 0 0 0 1 1 1 0 1 0 0 0 0 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 0 1 0 1 0 1 0 1 1 1 1 Nasonia_vitripennis
+1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 0 1 0 1 0 1 1 0 1 0 1 0 0 0 1 1 1 1 0 0 0 0 1 0 0 0 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 1 0 1 0 0 0 1 0 1 0 0 0 0 0 0 1 1 0 0 0 0 Oncometopia_nigricans
+1 1 0 1 1 0 0 1 1 1 0 1 1 1 1 0 1 0 1 0 1 1 0 1 0 1 1 0 0 1 1 0 1 1 1 1 1 0 1 1 1 0 0 1 1 1 1 0 1 0 1 1 0 1 0 0 1 1 0 1 1 1 1 1 1 0 1 0 0 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 0 0 0 0 1 1 1 1 1 1 1 1 Onychiurus_arcticus
+0 1 1 1 1 1 0 1 1 0 0 1 1 0 0 1 1 0 1 1 0 1 1 1 1 1 0 1 1 0 1 1 1 1 1 1 1 1 0 0 0 1 0 0 0 1 1 0 0 0 1 1 0 1 0 1 0 0 0 1 1 0 0 0 0 0 0 0 0 1 0 1 0 0 1 1 0 0 1 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 1 1 1 Pachypsylla_venusta
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 Pediculus_humanus
+1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 0 0 1 1 1 1 1 1 0 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 0 0 1 0 0 0 1 0 1 1 0 1 1 1 1 0 1 0 0 0 1 1 0 1 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0 Penaeus_monodon
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 0 0 1 0 1 1 1 0 0 1 0 1 0 0 1 1 1 0 0 0 0 0 0 1 1 0 1 0 0 1 1 0 1 0 0 1 0 0 1 0 0 0 1 1 1 1 0 0 0 0 0 1 1 1 1 0 1 1 0 0 1 0 0 1 1 1 0 Peripatopsis_sedgwicki
+1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 0 0 0 1 1 1 1 0 1 1 0 0 0 0 0 1 0 0 1 0 0 1 0 0 1 1 1 1 0 0 1 0 1 0 1 0 0 0 0 0 1 1 0 0 1 0 1 1 0 1 1 0 0 0 0 0 0 0 1 1 0 0 1 0 0 1 0 1 0 Periplaneta_americana
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 Petrolisthes_cinctipes
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 Phlebotomus_papatasi
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 0 1 1 1 1 0 1 1 1 1 1 0 1 0 0 0 0 0 0 1 0 0 0 0 1 0 Plodia_interpunctella
+1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 1 0 1 1 0 0 0 1 1 0 1 1 1 0 0 0 0 0 1 0 1 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 1 1 0 1 0 Plutella_xylostella
+1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 0 1 1 0 0 0 1 1 0 0 1 1 0 0 1 1 1 0 0 1 0 0 1 0 0 0 0 0 0 0 1 1 1 0 1 0 0 0 1 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 1 0 Pollicipes_pollicipes
+1 1 0 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 0 1 1 0 1 0 1 1 1 1 1 0 0 1 1 1 1 1 1 0 1 1 1 1 1 0 1 0 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 1 0 1 0 0 1 1 0 1 1 1 0 1 1 1 1 0 1 0 0 1 0 0 1 1 Rhipicephalus_appendiculatus
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 1 0 1 1 0 0 0 1 1 0 0 1 1 0 1 1 0 1 1 0 1 0 0 1 1 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 1 1 0 0 1 1 0 0 1 0 0 0 0 0 Rhynchosciara_americana
+1 0 1 1 1 1 0 0 1 1 1 1 0 1 1 1 1 1 0 0 1 0 1 0 1 1 1 1 0 1 1 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 1 1 1 1 1 0 0 0 0 1 0 0 1 0 1 1 0 0 0 0 1 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 Richtersius_coronifer
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 0 1 1 0 1 1 1 1 1 0 1 1 1 1 1 0 0 0 1 1 1 0 1 1 1 1 1 1 Samia_cynthia_ricini
+0 0 1 1 0 0 0 1 1 0 0 1 1 1 1 1 1 1 0 1 0 0 1 0 1 0 1 1 0 0 0 0 1 0 1 0 1 0 0 0 0 1 0 0 1 1 1 1 0 1 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 Scutigera_coleoptrata
+0 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 0 1 0 1 1 1 1 1 0 0 1 1 1 1 1 1 1 0 1 0 0 1 1 0 0 0 1 1 1 1 1 1 0 1 1 1 0 1 0 1 1 0 1 1 1 0 1 1 1 0 0 1 0 1 1 1 1 1 1 1 1 1 0 1 1 1 Solenopsis_invicta
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 Spodoptera_frugiperda
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 1 1 0 0 0 1 1 1 1 0 1 0 1 1 0 1 0 0 1 1 1 0 1 1 0 0 1 1 1 1 0 0 1 1 1 1 1 0 0 0 0 0 0 1 0 0 1 0 1 1 0 0 0 0 1 0 1 0 0 0 0 0 1 0 1 1 0 0 1 1 0 Suidasia_medanensis
+1 0 1 1 0 0 0 1 1 0 1 0 1 1 0 0 1 1 0 0 1 1 0 0 1 1 1 1 0 0 0 1 1 0 1 0 1 0 0 0 0 1 0 0 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 1 0 1 1 0 1 1 1 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 Tigriopus_californicus
+1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 0 0 1 1 0 1 1 0 1 1 0 1 1 0 0 0 1 0 1 1 0 0 0 0 1 1 0 1 1 1 0 0 0 1 0 1 1 0 1 1 1 0 1 1 0 1 1 1 1 0 1 0 0 0 1 0 1 0 1 0 0 1 0 0 Toxoptera_citricida
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Tribolium_castaneum
+1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 0 1 1 1 0 Trichinella_spiralis
+1 0 0 1 0 1 0 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 1 1 0 1 0 1 1 0 1 0 1 0 1 1 1 0 1 0 0 1 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 1 0 1 0 Triops_cancriformis
+1 0 1 1 0 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 0 0 0 0 1 0 1 0 1 1 0 0 0 1 1 1 0 1 1 0 0 1 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Vespula_squamosa
+1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 0 1 1 0 0 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 0 1 0 1 1 1 0 1 0 1 0 1 1 0 0 0 1 0 1 1 0 1 1 1 1 1 0 1 1 0 1 1 0 1 0 1 1 0 0 1 1 0 1 1 1 1 Xiphinema_index
=====================================
debian/tests/data/Meusemann.nwk
=====================================
@@ -0,0 +1 @@
+(((((Lysiphlebus_testaceipes,((Nasonia_giraulti,Nasonia_vitripennis),(Solenopsis_invicta,(Vespula_squamosa,Apis_mellifera)))),((Pediculus_humanus,((Locusta_migratoria,(Periplaneta_americana,(Hodotermopsis_sjoestedti,Blattella_germanica))),(Laupala_kohalensis,Gryllus_bimaculatus))),((((Maconellicoccus_hirsutus,((Myzus_persicae,Acyrthosiphon_pisum),(Aphis_gossypii,Toxoptera_citricida))),(Bemisia_tabaci,Pachypsylla_venusta)),((Homalodisca_coagulata,(Oncometopia_nigricans,Graphocephala_atropunctata)),Baetis_sp.)),(Ischnura_elegans,(Lepismachilis_y_signata,(((Acerentomon_franzi,Campodea_cf_fragilis),((Folsomia_candida,Anurida_maritima),Onychiurus_arcticus)),((Artemia_franciscana,(Triops_cancriformis,(Daphnia_magna,Daphnia_pulex))),(((Lepeophtheirus_salmonis,(Calanus_finmarchicus,Tigriopus_californicus)),(Pollicipes_pollicipes,(Gammarus_pulex,((Petrolisthes_cinctipes,(Homarus_americanus,(Carcinus_maenas,Callinectes_sapidus))),(Marsupenaeus_japonicus,((Penaeus_monodon,Litopenaeus_vannamei),Fenneropenaeus_chinensis)))))),((((Endeis_spinosa,Anoplodactylus_eroticus),((Acanthoscurria_gomesiana,Limulus_polyphemus),((Suidasia_medanensis,(Glycyphagus_domesticus,Blomia_tropicalis)),(Ixodes_scapularis,((Amblyomma_variegatum,Amblyomma_americanum),(Dermacentor_andersoni,(Rhipicephalus_appendiculatus,Boophilus_microplus))))))),((Euperipatoides_kanangrensis,Peripatopsis_sedgwicki),(((Lottia_gigantea,(Crassostrea_gigas,Argopecten_irradians)),(Capitella_capitata,(Helobdella_robusta,Lumbricus_rubellus))),((Richtersius_coronifer,Hypsibius_dujardini),((Xiphinema_index,Trichinella_spiralis),(Meloidogyne_hapla,((Haemonchus_contortus,((Caenorhabditis_remanei,Caenorhabditis_briggsae),Caenorhabditis_elegans)),Ascaris_suum))))))),(Archispirostreptus_gigas,Scutigera_coleoptrata)))))))))),(((((Danaus_plexippus,(((Heliconius_erato,Heliconius_melpomene),Bicyclus_anynana),Plodia_interpunctella)),((Spodoptera_frugiperda,(Helicoverpa_armigera,Heliothis_virescens)),(Manduca_sexta,(Bombyx_mori,((Antheraea_mylitta,Antheraea_assama),Samia_cynthia_ricini))))),Epiphyas_postvittana),Plutella_xylostella),((((Anopheles_albimanus,Anopheles_gambiae),((Armigeres_subalbatus,Aedes_aegypti),Culex_pipiens_quinquefasciatus)),(Culicoides_sonorensis,Chironomus_tentans)),(((Rhynchosciara_americana,Mayetiola_destructor),(Glossina_morsitans_morsitans,(((Drosophila_ananassae,(Drosophila_erecta,Drosophila_melanogaster)),Drosophila_arizonae),Ceratitis_capitata))),(Phlebotomus_papatasi,Lutzomyia_longipalpis))))),(Diaprepes_abbreviatus,(Leptinotarsa_decemlineata,Diabrotica_virgifera_virgifera))),Tribolium_castaneum);
\ No newline at end of file
=====================================
debian/tests/run-unit-test
=====================================
@@ -11,13 +11,19 @@ if [ "$AUTOPKGTEST_TMP" = "" ]; then
fi
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
cd "$AUTOPKGTEST_TMP"
-# Generate a random tree and matching occurrence data
+# Test 1: generated data - create a random tree and matching occurrence data
+# and count the terraces it spans.
/usr/lib/terraphast/tree_gen 6 > tree.nwk
/usr/lib/terraphast/site_gen 6 8 0.2 > data.txt
-
-# Enumerate terraces in phylogenetic tree space
/usr/lib/terraphast/validated_run count tree.nwk data.txt > /dev/null
+# Test 2: real-world data - the Meusemann insect phylogenomics dataset
+# (117 taxa, 97 sites), see README in this directory for its origin.
+/usr/lib/terraphast/validated_run count Meusemann.nwk Meusemann.data > /dev/null
+/usr/lib/terraphast/validated_run enumerate Meusemann.nwk Meusemann.data > /dev/null
+
echo "test passed"
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+Bug-Database: https://github.com/amkozlov/terraphast-one/issues
Reference:
- Author: Michael J. Sanderson and Michelle M. McMahon and Mike Steel
Title: Terraces in phylogenetic tree space
@@ -9,4 +10,5 @@ Reference:
DOI: 10.1126/science.1206357
PMID: 21680810
URL: https://www.science.org/doi/10.1126/science.1206357
+Repository: https://github.com/amkozlov/terraphast-one.git
Repository-Browse: https://github.com/amkozlov/terraphast-one
View it on GitLab: https://salsa.debian.org/med-team/terraphast/-/compare/7b906bf28e232e09a9c3aec6acd58451827e4be7...c5db3e8bed79bada5360223642645fde1ee10dbf
--
View it on GitLab: https://salsa.debian.org/med-team/terraphast/-/compare/7b906bf28e232e09a9c3aec6acd58451827e4be7...c5db3e8bed79bada5360223642645fde1ee10dbf
You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20261017/525c5002/attachment-0001.htm>
More information about the debian-med-commit
mailing list