overview

Full alignments, reports, and in some cases input files, results, and discussion for several datasets are available below. Additional datasets from collaborator or others who have aligned using the jrna format are listed as well.

!! As of March 4/2014 the site is now completely unpreviously locked, and is unmaintained. If you want your data to be hidden or removed please contact .

models / alignments

Taxon Gene(s) Taxa Partitions (bracketed) Columns Helices Mask pairs Reference/Source Availability
Gammaproteobacteria 16S 108 212 (7) 1677 (1528/149) 56 475 Williams et al. 2009 previously locked
Gammaproteobacteria 23S 108 473 (29) 3536 (2805/731) 126 817 Williams et al. 2009 previously locked
Arthropoda 18S 175 342 (84) 5019 (1819/3170) 148 549 J. J. Gillespie et al., 2005. available
Insecta Jon Mallat previously locked
Hymenoptera 28S D2-D3 84 103 (29) 487 (307/487) 25 146 Yoder, Gillespie, expanding Downton and Austin (2001) contact to view
Hymenoptera 18S 286 292 (241) 2128 (1887/241) 72 556 Yoder, Gillespie internal only
Hymenoptera 28S/18S HymATOL team available
Honeybee rDNA (Hymenoptera: Apidae) Gillespie available
Ichneumonoidea (Hymenoptera) 28S D2-D10; 18S 290 665 (100) 4912 149 1025 Gillespie, Yoder, Wharton, 2005 available
Exodontiella (Hymenoptera: Braconidae) 28S 59 112 (9) 566 (517/49) 27 144 Wharton et al. 2006 available
Chalcidoidea (Hymenoptera) 28S D2-D3 527 226 (59) 1417 (925/492) 50 282 Gillespie et al.2005 available
Chalcidoidea II (Hymenoptera) 28S D2-D3, 18S (partial) 525 James Munro (UCR) contact James
Azotinae (Hymenoptera: Chalcidoidea) 28S D2-D3; 18S 174 273 (66) 1778 (1129/649) 120 331 James Munro (UCR) contact James
Evaniidae (Hymenoptera: Evanioidea) 28S D2, 16S 60 212 (149) 2648 (2000/648) 45 250 Deans, Gillespie, and Yoder. 2006 available
Encyrtidae (Hymenoptera: Chalcidoidea) 28S D2-D3 116 138 (44) 985 (613/372) 64 208 Noyes et al. previously locked
Diapriidae (Hymenoptera: Proctotrupoidea) 28S, 18S 168 987 (54) 7089 (6111/978) 249 1705 Yoder and Gillespie, in prep previously locked
Scarabaeoidea (Coleoptera) 28S D2-D3 23 Marvaldi, Ocampo & Ruiz-Manzanos available
Phytophaga(Coleoptera) 28S, 18S 104 not calculated not calculated not calculated not calculated Marvaldi et al. 2008 available
Culicidae 16S 11 73 (0) (429/0) 12 88 Gillespie, unpublished previously locked
Scolytidae (Coleoptera) 28S D2-D5 109 219 (41) 1630 (1052/578) 50 340 Cognato, Gillespie available
Galerucinae - Structure Models (Coleoptera: Chrysomelidae) 28S D2-D3 Gillespie et al. 2004b available
Galerucinae - Alignments (Coleoptera: Chrysomelidae) 28S D2-D3 231 146 (29) 854 (683/171) 33 201 Gillespie et al. 2004b previously locked
Galerucinae - Alignment 2 (Coleoptera: Chrysomelidae) 28S D2-D3 249 322 (41) 2648 (2143/505) 72 467 Gillespie previously locked
Deuterostomes Jon Mallat in prep