[PRE REVIEW]: Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments

[whedon]

Submitting author: @marekborowiec (Marek Borowiec)
Repository: https://github.com/marekborowiec/spruceup
Version: v2019.1.1
Editor: @csoneson
Reviewers: @iimog, @gavinmdouglas

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1616 with the following error:

Could not find bibliography file: master.bib
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[labarba]

@marekborowiec — I am the Associate Editor-in-Chief on rotation this week, and will be working to identify an editor to handle your submission. But first, you need to add a paper.bib file with the references cited in your paper, in BibTeX format.

[marekborowiec]

Ah yes. Done.

[labarba]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1616 with the following error:

Could not find bibliography file: master.bib
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[labarba]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1616 with the following error:

Could not find bibliography file: master.bib
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[labarba]

Please merge this fix
marekborowiec/spruceup#1

[labarba]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[marekborowiec]

Seems like I didn't set the figure caption correctly. Please try again.

[labarba]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[labarba]

👋 @csoneson — the submitting author suggested you as handling editor. Could you take this one?

Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments
https://github.com/marekborowiec/spruceup
Article proof 📄

[csoneson]

@whedon assign @csoneson as editor

[whedon]

OK, the editor is @csoneson

[csoneson]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- 10.1093/molbev/msu236 is OK
- 10.1016/j.ympev.2019.02.012 is OK
- 10.1134/s0869593808030052 is OK
- 10.1134/s1022795416080020 is OK
- 10.1016/j.ympev.2014.10.011 is OK
- 10.1016/j.ympev.2016.10.016 is OK
- 10.1016/j.cub.2015.12.060 is OK
- 10.1371/journal.pone.0129183 is OK
- 10.1093/sysbio/syv027 is OK
- 10.1093/sysbio/syw022 is OK
- 10.1007/s00040-005-0808-y is OK
- 10.1007/s00040-007-0932-y is OK
- 10.1111/ele.12438 is OK
- 10.1111/mec.14183 is OK
- 10.1111/j.1420-9101.2008.01531.x is OK
- 10.1111/j.1096-0031.2005.00059.x is OK
- 10.1016/j.ympev.2012.08.023 is OK
- 10.1093/sysbio/syt073 is OK
- 10.1186/s12862-015-0552-5 is OK
- 10.1371/journal.pone.0161531 is OK
- 10.1093/molbev/msn018 is OK
- 10.1002/0471142905.hg1804s66 is OK
- 10.1101/407452 is OK
- 10.1093/bioinformatics/btu170 is OK
- 10.1093/oxfordjournals.molbev.a004175 is OK
- 10.1126/science.1192428 is OK
- 10.3897/zookeys.133.1479 is OK
- 10.1186/s12864-015-2146-4 is OK
- 10.4289/0013-8797.117.1.62 is OK
- 10.1186/s12864-015-2146-4 is OK
- 10.7717/peerj.1660 is OK
- 10.7717/peerj.1660 is OK
- 10.3897/zookeys.608.9427 is OK
- 10.3897/zookeys.608.9427 is OK
- 10.1093/sysbio/syy088 is OK
- 10.1371/journal.pcbi.1003537 is OK
- 10.1111/syen.12181 is OK
- 10.1073/pnas.1137809100 is OK
- 10.1111/j.1365-3113.2005.00290.x is OK
- 10.1186/1471-2148-14-93 is OK
- 10.1101/039966 is OK
- 10.1111/2041-210x.12742 is OK
- 10.1016/j.cub.2017.03.027 is OK
- 10.1111/jbi.12310 is OK
- 10.1093/bioinformatics/btn651 is OK
- 10.1093/sysbio/syu009 is OK
- 10.1093/sysbio/syx074 is OK
- 10.1093/sysbio/syw101 is OK
- 10.1186/1471-2105-10-421 is OK
- 10.1093/bioinformatics/btp348 is OK
- 10.1111/mec.12413 is OK
- 10.1007/978-3-540-35306-5_10 is OK
- 10.4137/ebo.s40583 is OK
- 10.1111/cla.12099 is OK
- 10.1093/bioinformatics/btp163 is OK
- 10.1371/journal.pone.0104410 is OK
- 10.1046/j.1365-2699.2001.00566.x is OK
- 10.1186/1471-2148-10-210 is OK
- 10.1146/annurev-ento-120811-153643 is OK
- 10.1093/bioinformatics/btr330 is OK
- 10.1080/10635150701701083 is OK
- 10.1371/journal.pbio.1002033 is OK
- 10.1038/nrg1603 is OK
- 10.1186/s12862-019-1350-2 is OK
- 10.1098/rstb.2016.0020 is OK
- 10.1093/molbev/msr045 is OK
- 10.1093/molbev/msr045 is OK
- 10.1098/rspb.2012.0683 is OK
- 10.1093/sysbio/syy001 is OK
- 10.1093/sysbio/syv041 is OK
- 10.1186/1748-7188-3-7 is OK
- 10.1186/1471-2148-7-214 is OK
- 10.1111/jbi.12592 is OK
- 10.1111/j.1558-5646.2008.00549.x is OK
- 10.1016/j.ympev.2015.10.027 is OK
- 10.1098/rspb.2016.1529 is OK
- 10.6079/J9ILL is OK
- 10.1371/journal.pone.0042543 is OK
- 10.1371/journal.pone.0042543 is OK
- 10.1093/sysbio/sys004 is OK
- 10.1111/1755-0998.12328 is OK
- 10.1093/bioinformatics/btv646 is OK
- 10.1111/2041-210x.12754 is OK
- 10.1093/sysbio/27.4.401 is OK
- 10.1002/joc.5086 is OK
- 10.1186/gb-2011-12-1-r1 is OK
- 10.1093/molbev/msy224 is OK
- 10.1007/pl00006471 is OK
- 10.1080/10635150490445779 is OK
- 10.1186/s12862-015-0283-7 is OK
- 10.1093/sysbio/syt033 is OK
- 10.1371/journal.pcbi.1002984 is OK
- 10.1111/mec.13108 is OK
- 10.1073/pnas.1715318114 is OK
- 10.1073/pnas.1715318114 is OK
- 10.1101/461699 is OK
- 10.1371/journal.pcbi.1003919 is OK
- 10.1016/j.ympev.2018.08.007 is OK
- 10.13102/sociobiology.v65i3.3315 is OK
- 10.1093/sysbio/syv028 is OK
- 10.1016/j.ympev.2003.11.016 is OK
- 10.1016/j.ympev.2016.09.008 is OK
- 10.1038/nbt.1883 is OK
- 10.1098/rstb.1989.0106 is OK
- 10.1007/s00040-018-0625-8 is OK
- 10.1007/s00040-018-0625-8 is OK
- 10.1093/sysbio/syq010 is OK
- 10.1093/annonc/mdy166 is OK
- 10.1093/nar/gkt371 is OK
- 10.1111/evo.12832 is OK
- 10.1016/j.ympev.2013.11.007 is OK
- 10.1186/s12862-016-0769-y is OK
- 10.1073/pnas.1617397114 is OK
- 10.1111/2041-210x.12949 is OK
- 10.1038/361023b0 is OK
- 10.1073/pnas.1319091111 is OK
- 10.1371/journal.pone.0131023 is OK
- 10.1186/s12859-016-1277-1 is OK
- 10.1007/978-3-030-00834-5_14 is OK
- 10.2307/2992396 is OK
- 10.1093/sysbio/syp035 is OK
- 10.1093/molbev/msx281 is OK
- 10.1093/molbev/msr095 is OK
- 10.1038/nrg1044 is OK
- 10.1111/j.1365-2311.2008.01005.x is OK
- 10.1093/sysbio/42.3.247 is OK
- 10.4137/ebo.s9017 is OK
- 10.1126/science.231.4734.129 is OK
- 10.1093/sysbio/syw117 is OK
- 10.1093/sysbio/syx001 is OK
- 10.1016/j.ympev.2004.07.012 is OK
- 10.1016/j.ympev.2010.01.029 is OK
- 10.1093/sysbio/syu036 is OK
- 10.1186/s12859-015-0702-1 is OK
- 10.1080/10635150490468648 is OK
- 10.7717/peerj.5024 is OK
- 10.1093/molbev/mst010 is OK
- 10.1086/650369 is OK
- 10.1111/j.1558-5646.2012.01663.x is OK
- 10.1016/j.cois.2016.09.006 is OK
- 10.1093/molbev/msi203 is OK
- 10.1098/rspb.2002.2288 is OK
- 10.1186/1471-2148-7-56 is OK
- 10.1186/1742-9994-7-10 is OK
- 10.1371/journal.pone.0060019 is OK
- 10.1093/molbev/msw260 is OK
- 10.1098/rstb.2014.0338 is OK
- 10.1038/nature14539 is OK
- 10.1111/mec.13170 is OK
- 10.1093/bioinformatics/btp324 is OK
- 10.1126/science.1171243 is OK
- 10.1073/pnas.1715371114 is OK
- 10.1073/pnas.1616744114 is OK
- 10.1371/journal.pone.0084012 is OK
- 10.1016/j.cois.2016.09.007 is OK
- 10.1186/s12864-018-4620-2 is OK
- 10.1002/bies.201500149 is OK
- 10.1371/journal.pone.0192011 is OK
- 10.1111/j.0014-3820.2002.tb00844.x is OK
- 10.1186/1471-2148-8-237 is OK
- 10.1371/journal.pone.0103800 is OK
- 10.1016/j.ympev.2018.02.007 is OK
- 10.1093/sysbio/syu056 is OK
- 10.1111/1755-0998.12466 is OK
- 10.1007/978-1-4613-3485-9_19 is OK
- 10.1101/gr.107524.110 is OK
- 10.1111/evo.13378 is OK
- 10.1111/evo.13574 is OK
- 10.1109/gce.2010.5676129 is OK
- 10.1093/molbev/mst024 is OK
- 10.1101/487801 is OK
- 10.1093/sysbio/syu063 is OK
- 10.1126/science.1250463 is OK
- 10.1093/bioinformatics/btv234 is OK
- 10.1038/s41467-018-08089-7 is OK
- 10.1073/pnas.1518659113 is OK
- 10.3390/computation3020177 is OK
- 10.1093/molbev/mst117 is OK
- 10.1111/j.1558-5646.2008.00501.x is OK
- 10.1073/pnas.0801464105 is OK
- 10.1111/mec.14431 is OK
- 10.1101/460121 is OK
- 10.1007/s13127-015-0215-9 is OK
- 10.1093/molbev/msu300 is OK
- 10.1186/s13059-015-0688-z is OK
- 10.1101/gr.121392.111 is OK
- 10.1038/ncomms12233 is OK
- 10.1080/10635150500541730 is OK
- 10.1016/j.cub.2014.01.018 is OK
- 10.1093/bioinformatics/btg412 is OK
- 10.1016/j.ympev.2013.02.008 is OK
- 10.1111/j.0014-3820.2002.tb00128.x is OK
- 10.1002/ajb2.1016 is OK
- 10.1073/pnas.1804098115 is OK
- 10.1093/nar/gkq443 is OK
- 10.1890/07-1295.1 is OK
- 10.1016/j.cub.2017.01.027 is OK
- 10.1007/pl00006573 is OK
- 10.1186/1741-7007-9-91 is OK
- 10.5852/ejt.2017.283 is OK
- 10.1186/s12862-017-1095-8 is OK
- 10.1111/mec.13799 is OK
- 10.1073/pnas.0806187105 is OK
- 10.1371/journal.pone.0006781 is OK
- 10.1111/j.1365-3113.2010.00533.x is OK
- 10.1073/pnas.1105467108 is OK
- 10.3099/mcz3.1 is OK
- 10.1007/s12686-013-0078-3 is OK
- 10.1146/annurev-ento-120811-153710 is OK
- 10.1007/s12686-014-0204-x is OK
- 10.1016/j.cub.2014.07.048 is OK
- 10.1007/s00040-015-0406-6 is OK
- 10.3897/zookeys.618.9692 is OK
- 10.1371/journal.pone.0089543 is OK
- 10.1111/2041-210x.12199 is OK
- 10.1111/bij.12703 is OK
- 10.1093/sysbio/syx037 is OK
- 10.1111/evo.13566 is OK
- 10.1534/genetics.114.164350 is OK
- 10.3389/fpls.2017.01852 is OK
- 10.1371/journal.pone.0138446 is OK
- 10.1007/s00040-002-8288-9 is OK
- 10.1086/676505 is OK
- 10.1093/sysbio/syv016 is OK
- 10.1080/10635150701397643 is OK
- 10.1101/gr.128124.111 is OK
- 10.1093/molbev/mst116 is OK
- 10.1093/molbev/msv258 is OK
- 10.1186/s12862-018-1159-4 is OK
- 10.1093/sysbio/sys029 is OK
- 10.1038/nature12130 is OK
- 10.1093/oxfordjournals.molbev.a003974 is OK
- 10.1111/jzs.12184 is OK
- 10.1006/bijl.2001.0542 is OK
- 10.3391/bir.2014.3.4.13 is OK
- 10.1093/sysbio/syt041 is OK
- 10.1073/pnas.1036825100 is OK
- 10.1093/molbev/msw079 is OK
- 10.1016/j.ympev.2018.01.019 is OK
- 10.2307/1538043 is OK
- 10.1111/j.0307-6946.2005.00720.x is OK
- 10.1038/ncomms6495 is OK
- 10.1016/j.tig.2017.12.005 is OK
- 10.1007/s10682-010-9371-8 is OK
- 10.1038/s41559-017-0126 is OK
- 10.1016/j.ympev.2015.05.011 is OK
- 10.1016/j.ympev.2015.12.013 is OK
- 10.1016/j.ympev.2018.10.001 is OK
- 10.1086/699515 is OK
- 10.1073/pnas.1008617108 is OK
- 10.1073/pnas.1007901108 is OK
- 10.1093/molbev/msv165 is OK
- 10.1101/356345 is OK
- 10.1371/journal.pone.0080498 is OK
- 10.1371/journal.pone.0176498 is OK
- 10.1007/s00040-017-0550-2 is OK
- 10.1111/syen.12289 is OK
- 10.1007/978-1-4614-6846-2_2 is OK
- 10.1016/j.ympev.2015.07.018 is OK
- 10.1093/jhered/esx089 is OK
- 10.1093/jhered/esx089 is OK
- 10.1080/14772000.2017.1401016 is OK
- 10.1080/14772000.2017.1401016 is OK
- 10.1093/bioinformatics/btu033 is OK
- 10.1017/cbo9781107261402.002 is OK
- 10.1017/cbo9781107261402 is OK
- 10.1371/journal.pgen.1002007 is OK
- 10.1093/bioinformatics/btq228 is OK
- 10.1111/mec.15029 is OK
- 10.1101/559054 is OK
- 10.1093/molbev/msy069 is OK
- 10.1093/gbe/evw071 is OK
- 10.1080/10635150701472164 is OK
- 10.1093/sysbio/syv033 is OK
- 10.1007/bf01240430 is OK
- 10.1186/1471-2164-16-s10-s3 is OK
- 10.1016/j.ympev.2018.03.006 is OK
- 10.1186/s12859-016-1146-y is OK
- 10.1186/1471-2105-15-s2-s8 is OK
- 10.1093/sysbio/syy043 is OK
- 10.1111/syen.12090 is OK
- 10.1098/rspb.2014.1257 is OK
- 10.1007/s10955-018-1975-3 is OK
- 10.1093/bioinformatics/bty448 is OK
- 10.1371/journal.pone.0030288 is OK
- 10.1073/pnas.1009690108 is OK
- 10.1186/s13059-019-1689-0 is OK
- 10.1093/molbev/msj024 is OK
- 10.1093/molbev/msm088 is OK
- 10.1093/molbev/msm088 is OK
- 10.1093/molbev/msu245 is OK
- 10.3109/19401736.2015.1018229 is OK
- 10.1111/mec.13813 is OK
- 10.1093/sysbio/syv080 is OK
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- 10.1038/s41588-018-0295-5 is OK

MISSING DOIs

- https://doi.org/10.1111/j.1365-3113.1994.tb00581.x may be missing for title: The phylogeny of the ant tribe Formicini (Hymenoptera: Formicidae) with the description of a new genus
- https://doi.org/10.1134/s0869593808030052 may be missing for title: Palynological characteristics of Upper Cretaceous and Paleogene deposits on the west of the Sambian Peninsula (Kaliningrad region), Part 2
- https://doi.org/10.1134/s1062359016010027 may be missing for title: New approaches for reconstruction of the ecosystem of an Eocene amber forest
- https://doi.org/10.1038/s41598-018-20262-y may be missing for title: Comparative analyses of co-evolving host-parasite associations reveal unique gene expression patterns underlying slavemaker raiding and host defensive phenotypes
- https://doi.org/10.1086/283557 may be missing for title: The origins of slavery in leptothoracine ants (Hymenoptera: Formicidae)
- https://doi.org/10.15298/rusentj.20.3.02 may be missing for title: A new tribe of fossil digger wasps (Hymenoptera: Crabronidae) from the Upper Cretaceous New Jersey amber and its place in the subfamily Pemphredoninae
- https://doi.org/10.1603/0013-8746(2006)99[487:baoteo]2.0.co;2 may be missing for title: Bulldog Ants of the Eocene Okanagan Highlands and History of the Subfamily (Hymenoptera: Formicidae: Myrmeciinae)
- https://doi.org/10.11646/zootaxa.2870.1.3 may be missing for title: Fossil Ponerinae (Hymenoptera: Formicidae) in Early Eocene amber of France
- https://doi.org/10.5962/bhl.title.13535 may be missing for title: The Naturalist on the River Amazons: a Record of Adventures, Habits of Animals, Sketches of Brazilian and Indian Life, and Aspects of Nature Under the Equator, During Eleven Years of Travel. With a Memoir of the Author, by Edward Clodd
- https://doi.org/10.3409/173491505783995608 may be missing for title: A primitive sapygid wasp in Burmese amber (Hymenoptera: Sapygidae)
- https://doi.org/10.1080/00222939000770811 may be missing for title: Army ants reassessed: the phylogeny and classification of the doryline section (Hymenoptera, Formicidae)
- https://doi.org/10.5860/choice.32-2110 may be missing for title: Identification guide to the ant genera of the world
- https://doi.org/10.5852/ejt.2015.120 may be missing for title: Contributions to the knowledge of Formicidae (Hymenoptera, Aculeata): a new diagnosis of the family, the first global male-based key to subfamilies, and a treatment of early branching lineages
- https://doi.org/10.1111/j.1095-8312.1991.tb00591.x may be missing for title: Alternative adaptations, sympatric speciation and the evolution of parasitic, inquiline ants
- https://doi.org/10.1073/pnas.0605858103 may be missing for title: Evaluating alternative hypotheses for the early evolution and diversification of ants
- https://doi.org/10.1017/s1464793104006669 may be missing for title: The coevolutionary dynamics of obligate ant social parasite systems–between prudence and antagonism
- https://doi.org/10.1214/ss/1009213726 may be missing for title: Statistical modeling: The two cultures (with comments and a rejoinder by the author)
- https://doi.org/10.1016/0169-5347(86)90044-3 may be missing for title: Evolution of social parasitism in ants
- https://doi.org/10.1111/j.1439-0469.1990.tb00379.x may be missing for title: Sympatric speciation and radiative evolution of socially parasitic ants - Heretic hypotheses and their factual background
- https://doi.org/10.1093/sysbio/syw037 may be missing for title: Terrace aware data structure for phylogenomic inference from supermatrices
- https://doi.org/10.1109/cvprw.2009.5206848 may be missing for title: ImageNet: A large-scale hierarchical image database
- https://doi.org/10.1007/s102110100038 may be missing for title: Sociobiology of slave-making ants
- https://doi.org/10.1134/s0031030108050055 may be missing for title: Ants of the tribe Formicini (Hymenoptera, Formicidae) from late Eocene amber of Europe
- https://doi.org/10.4202/app.2008.0406 may be missing for title: New middle Eocene formicid species from Germany and the evolution of weaver ants
- https://doi.org/10.1134/s0031030109090056 may be missing for title: Ants (Insecta: Vespida: Formicidae) in the Upper Eocene amber of central and eastern Europe
- https://doi.org/10.1134/s0031030109090068 may be missing for title: The ant subfamilies Ponerinae, Cerapachyinae, and Pseudomyrmecinae (Hymenoptera, Formicidae) in the Late Eocene Ambers of Europe
- https://doi.org/10.23885/1814-3326-2015-11-1-131-152 may be missing for title: The ants (Hymenoptera: Formicidae) of Bol’shaya Svetlovodnaya (Late Eocene of Sikhote-Alin, Russian Far East)
- https://doi.org/10.1111/jbi.12898 may be missing for title: Bayesian estimation of the global biogeographical history of the Solanaceae
- https://doi.org/10.1073/pnas.0607004104 may be missing for title: High-resolution species trees without concatenation
- https://doi.org/10.5860/choice.50-4435 may be missing for title: A field guide to the ants of New England
- https://doi.org/10.2317/jkes-712.11.1 may be missing for title: The wasp family Rhopalosomatidae in mid-Cretaceous amber from Myanmar (Hymenoptera: Vespoidea)
- https://doi.org/10.1660/062.112.0201 may be missing for title: A remarkable tiphiiform wasp in mid-Cretaceous amber from Myanmar (Hymenoptera: Tiphiidae)
- https://doi.org/10.1186/s12862-017-1078-9 may be missing for title: Species-specific genes under selection characterize the co-evolution of slavemaker and host lifestyles
- https://doi.org/10.1098/rspb.2001.1627 may be missing for title: Coevolution in host–parasite systems: behavioural strategies of slave–making ants and their hosts
- https://doi.org/10.1093/oxfordjournals.molbev.a025808 may be missing for title: BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
- https://doi.org/10.1093/aesa/72.4.462 may be missing for title: Phylogenetic implications of army ant zoogeography (Hymenoptera: Formicidae)
- https://doi.org/10.1093/aesa/89.2.309 may be missing for title: Army ants: the biology of social predation
- https://doi.org/10.1073/pnas.240452097 may be missing for title: A formicine in New Jersey Cretaceous amber (Hymenoptera: Formicidae) and early evolution of the ants
- https://doi.org/10.5962/bhl.title.49948 may be missing for title: Recherches sur les moeurs des fourmis indigènes
- https://doi.org/10.1038/nmeth.4285 may be missing for title: ModelFinder: fast model selection for accurate phylogenetic estimates
- https://doi.org/10.1111/j.1469-185x.2010.00173.x may be missing for title: Cuckoos versus hosts in insects and birds: adaptations, counter-adaptations and outcomes
- https://doi.org/10.1145/3065386 may be missing for title: ImageNet Classification with Deep Convolutional Neural Networks
- https://doi.org/10.13102/sociobiology.v62i2.163-174 may be missing for title: Fossil ants (Hymenoptera: Formicidae) of the Middle Eocene Kishenehn Formation
- https://doi.org/10.1093/bioinformatics/btu531 may be missing for title: AliView: a fast and lightweight alignment viewer and editor for large datasets
- https://doi.org/10.2307/3494827 may be missing for title: Zoogeography of Caribbean insects
- https://doi.org/10.1111/evo.12161 may be missing for title: Origins, evolution, and diversification of cleptoparasitic lineages in long-tongued bees
- https://doi.org/10.1093/oxfordjournals.molbev.a040136 may be missing for title: Recovering evolutionary trees under a more realistic model of sequence evolution.
- https://doi.org/10.21425/f5fbg19694 may be missing for title: Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing
- https://doi.org/10.3140/bull.geosci.1425 may be missing for title: New ants (Hymenoptera: Formicidae: Dolichoderinae) from Canadian Late Cretaceous amber
- https://doi.org/10.1126/science.1124891 may be missing for title: Phylogeny of the ants: diversification in the age of angiosperms
- https://doi.org/10.1111/evo.12105 may be missing for title: Testing the museum versus cradle tropical biological diversity hypothesis: phylogeny, diversification, and ancestral biogeographic range evolution of the ants
- https://doi.org/10.11646/zootaxa.2870.1.3 may be missing for title: Fossil Ponerinae (Hymenoptera: Formicidae) in Early Eocene amber of France
- https://doi.org/10.1007/s00114-007-0301-8 may be missing for title: Fossil evidence for the early ant evolution
- https://doi.org/10.1111/j.1463-6409.2008.00340.x may be missing for title: Molecular phylogenetics of Vespoidea indicate paraphyly of the superfamily and novel relationships of its component families and subfamilies
- https://doi.org/10.1126/science.1134103 may be missing for title: A fossil bee from Early Cretaceous Burmese amber
- https://doi.org/10.1086/284901 may be missing for title: Intraspecific brood raiding, territoriality, and slavery in ants
- https://doi.org/10.1515/9781400840809 may be missing for title: Evolutionary ecology of parasites
- https://doi.org/10.1017/s0031182006002150 may be missing for title: Are there general laws in parasite ecology?
- https://doi.org/10.1073/pnas.0806187105 may be missing for title: Newly discovered sister lineage sheds light on early ant evolution
- https://doi.org/10.1111/j.1096-3642.1999.tb00596.x may be missing for title: Giant ants from the Paleogene of Denmark with a discussion of the fossil history and early evolution of ants (Hymenoptera: Formicidae)
- https://doi.org/10.1111/j.1095-8312.1996.tb01695.x may be missing for title: Facultative and obligate slavery in formicine ants: frequency of slavery, and proportion and size of slaves
- https://doi.org/10.1093/molbev/msx261 may be missing for title: Fragmentary gene sequences negatively impact gene tree and species tree reconstruction
- https://doi.org/10.1111/jbi.13380 may be missing for title: Do Holarctic ant species exist? Trans-Beringian dispersal and homoplasy in the Formicidae
- https://doi.org/10.11646/zootaxa.3647.2.1 may be missing for title: Molecular phylogenetics of ponerine ants (Hymenoptera: Formicidae: Ponerinae)
- https://doi.org/10.1111/bij.12043 may be missing for title: Repeated origins of social parasitism in allodapine bees indicate that the weak form of Emery’s rule is widespread, yet sympatric speciation remains highly problematic
- https://doi.org/10.1126/science.215.4537.1262 may be missing for title: Territoriality and the origin of slave raiding in leptothoracine ants
- https://doi.org/10.1093/nar/25.24.4876 may be missing for title: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
- https://doi.org/10.1093/sysbio/syq012 may be missing for title: Phylogeny and biogeography of dolichoderine ants: effects of data partitioning and relict taxa on historical inference
- https://doi.org/10.1111/syen.12186 may be missing for title: Tales of dracula ants: the evolutionary history of the ant subfamily Amblyoponinae (Hymenoptera: Formicidae)
- https://doi.org/10.1111/j.1469-185x.1987.tb01640.x may be missing for title: The roles of seasonality, host synchrony, and behaviour in the evolutions and distributions of nest parasites in Hymenoptera (Insecta). With special reference to bees (Apoidea)
- https://doi.org/10.1086/277964 may be missing for title: The compound and mixed nests of American ants. Part II. The known cases of social symbiosis among American ants
- https://doi.org/10.1155/1930/93593 may be missing for title: Two new ants from Java
- https://doi.org/10.1086/285570 may be missing for title: Diversification of carnivorous parasitic insects: extraordinary radiation or specialized dead end?
- https://doi.org/10.1038/scientificamerican0675-32 may be missing for title: Slavery in ants
- https://doi.org/10.1126/science.1059412 may be missing for title: Trends, rhythms, and aberrations in global climate 65 Ma to present
- https://doi.org/10.1186/s12859-018-2129-y may be missing for title: ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

INVALID DOIs

- None

[csoneson]

Ok, not exactly sure what just happened with the reference check, that looks a bit excessive...

Anyway - @marekborowiec, do you have suggestions for reviewers that would be suitable for your submission (e.g. from the list linked in the first post in this issue)?

While we are looking for reviewers, could you also fix a couple of small things in the paper:

• remove the "editor" line in the .bib entries
• be consistent in using either abbreviated or non-abbreviated journal names in the bibliography

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[csoneson]

👋 @iimog, @gavinmdouglas, @shaunpwilkinson, @giraola, @dsurujon, @Nazeeefa, @camillescott - would (two of) you be willing to review this submission for JOSS?

[iimog]

👋 @camillescott I'd be willing to review this submission.

[csoneson]

Thanks @iimog!

[csoneson]

@whedon assign @iimog as reviewer

[whedon]

OK, the reviewer is @iimog

[marekborowiec]

Is there a way to make the figure go before References?

[csoneson]

Is there a way to make the figure go before References?

Hm, making figures appear in the desired place in the output is certainly not always easy. From jgm/pandoc#845 I think you can override the default placement of the figure, and it is also possible to explicitly add \pagebreak to force a new page. Whether that will look better in the end remains to be seen. Btw, I'm not sure you need a separate section for the figure - could it just go in the paragraph where it is mentioned?

[arfon]

I would suggested waiting on fixing this issue until the submission is reviewed and accepted. Layouts are notoriously hard with Markdown/Pandoc and as the paper contents may change during review, we should just fix this once at the end.

Does that sounds reasonable to everyone?

[iimog]

@whedon start review

[whedon]

I'm sorry @iimog, I'm afraid I can't do that. That's something only editors are allowed to do.

[csoneson]

Hi @iimog - we're just waiting for one more reviewer, then I'll officially start the review; i.e., open the actual review issue, with the reviewer checklists etc. (of course, you can already start looking at the submission :))

[iimog]

Thanks @csoneson and sorry for being impatient :)

[marekborowiec]

I would suggested waiting on fixing this issue until the submission is reviewed and accepted.

Sounds good to me. I was just wondering if my markdown file was properly formatted.

[gavinmdouglas]

I'm familiar and interested in the topic although not an expert regarding alignment trimming - if that's ok then I'm happy to be a reviewer.

[csoneson]

Thank you @gavinmdouglas!

[csoneson]

@whedon add @gavinmdouglas as reviewer

[whedon]

OK, @gavinmdouglas is now a reviewer

[csoneson]

@whedon start review

[whedon]

OK, I've started the review over in #1635. Feel free to close this issue now!