Erick Matsen

My first thought was to throw geographic information in a second data partition. IQTree allows this: http://www.iqtree.org/doc/Complex-Models#partition-models . There aren't currently any completely custom models, but you can supply a...

We have * time * number of mutations that happened on branches (these are, practically-speaking, terminal mutations) * sampling location

Thanks, @afmagee ! I might also suggest two things: * this could merely supply a ranking of pairs of nodes to try, and how far down that list would be...

@huddlej were you thinking that the clustering would happen inside Java? If we were to do that we would probably want to bring in some library for that. An alternative,...

Hello-- for that specific error my guess is that you need to have an old version of GSL installed.

It works for me at https://matsen.github.io/pplacer/ . If this doesn't work for you, please try in a Private Browsing window.

Example: {"tree": "((Skeletonema_marinoiEST:0{0},Skeletonema_costatumEST:0{1}):0.07798{2},Thalassiosira_spEST:0.08822{3},(Thalassiosira_punctigeraEST:0.02457{4},(THALASSIOSIRA_OCEANICA_397628097NCBI:0.09418{5},(Detonula_confervaceaEST:0.10025{6},(Cyclotella_meneghinianaEST:0.02055{7},(((Coscinodiscus_wailesiiEST:0.18364{8},Aulacoseira_subarcticaEST:0.34004{9})0.890:0.07344{10},((Ditylum_brightwelliPop2EST:0.0744{11},(Odontella_spEST:0.12129{12},Minutocellus_polymorphusEST:0.1061{13})0.876:0.04964{14})0.884:0.0511{15},(GUILLARDIA_THETA_AF165818NCBI:1.10613{16},(Striatella_unipunctataEST:0.32178{17},((FRAGILARIOPSIS_CYLDRINUS64230JGI:0.09243{18},(Pseudo-nitzschia_arenysensisEST:0.11617{19},(PSEUDO-NITZSCHIA_MULTISERIES_303116JGI:0.04952{20},(Pseudo-nitzschia_pungensGGA1EST:0.00054{21},Pseudo-nitzschia_pungensGGC3EST:0.0172{22})0.877:0.03355{23})0.970:0.11857{24})0.868:0.0637{25})0.998:0.19409{26},(Cylindrotheca_closteriumEST:0.21291{27},(Amphiprora_spEST:0.25598{28},PHAEODACTYLUM_TRICORNUTUM_55112JGI:0.11808{29})0.937:0.11822{30})0.844:0.04978{31})0.328:0.02716{32})0.868:0.11524{33})0.674:0.03866{34})0.517:0.01677{35})0.984:0.11427{36},THALASSIOSIRA_PSEUDONANA_268343JGI:0.13032{37})0.484:0.02347{38})0.917:0.07817{39})0.445:0.03606{40})0.792:0.03328{41})0.848:0.04047{42}){43};", "placements": [ {"p": [[0, 0, -nan, -inf, 1.99999275208], [0, 1, -nan, -inf, 1.99999275208], [0.077970480957, 2, -nan, -inf, 1.99999275208], [0.0882146154785, 3, -nan, -inf, 1.99999275208], [0.0245640014648, 4, -nan, -inf,...

Hey there! As described above, there is one for https://github.com/matsen/pplacer/releases/tag/v1.1.alpha17 . The differences between alpha17 and alpha18 are not important for using CheckM.

Hey @rekado thanks for this! I've been away so am just catching up. Does this require pplacer code changes, or just packaging changes? If the former, would you like to...

Hello @AjitPS -- All pplacer releases have guppy in them. We stopped directly supporting RAxML output in pplacer ages ago. The modern way is to use a reference package made...