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

Created on 1 Aug 2019 · 52Comments · Source: openjournals/joss-reviews

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

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Thanks for submitting your paper to JOSS @marekborowiec. Currently, there isn't an JOSS editor assigned to your paper.

@marekborowiec if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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Most helpful comment

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?

arfon on 8 Aug 2019

👍2

All 52 comments

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

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whedon on 1 Aug 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 1 Aug 2019

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

whedon on 1 Aug 2019

@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.

labarba on 1 Aug 2019

Ah yes. Done.

marekborowiec on 1 Aug 2019

@whedon generate pdf

labarba on 1 Aug 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 1 Aug 2019

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

whedon on 1 Aug 2019

@whedon generate pdf

labarba on 1 Aug 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 1 Aug 2019

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

whedon on 1 Aug 2019

Please merge this fix
https://github.com/marekborowiec/spruceup/pull/1

labarba on 1 Aug 2019

@whedon generate pdf

labarba on 2 Aug 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 2 Aug 2019

:point_right: Check article proof :page_facing_up: :point_left:

whedon on 2 Aug 2019

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

marekborowiec on 3 Aug 2019

@whedon generate pdf

labarba on 3 Aug 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 3 Aug 2019

:point_right: Check article proof :page_facing_up: :point_left:

whedon on 3 Aug 2019

👋 @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 :page_facing_up:

labarba on 3 Aug 2019

👍1

@whedon assign @csoneson as editor

csoneson on 3 Aug 2019

OK, the editor is @csoneson

whedon on 3 Aug 2019

@whedon check references

csoneson on 3 Aug 2019

Attempting to check references...

whedon on 3 Aug 2019

```Reference check summary:

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
10.1186/1471-2148-11-369 is OK
10.1038/s41588-018-0295-5 is OK

MISSING DOIs

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https://doi.org/10.1093/aesa/89.2.309 may be missing for title: Army ants: the biology of social predation
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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
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https://doi.org/10.1111/evo.12161 may be missing for title: Origins, evolution, and diversification of cleptoparasitic lineages in long-tongued bees
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INVALID DOIs

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```

whedon on 3 Aug 2019

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

csoneson on 3 Aug 2019

I believe the following people should be able to review this:

@iimog, @gvegayon, @gavinmdouglas, @shaunpwilkinson, @giraola, @dsurujon, @Nazeeefa, @camillescott

I have also removed the editor line from bibliography entries for journal articles and attempted to make consistent use of unabbreviated journal names.

I also introduced a couple adjustments to the paper.md file so that it (hopefully) correctly renders the figure and references section title correctly.

marekborowiec on 6 Aug 2019

I'm sorry, but I'm not familiar with the topic, so I'm afraid I can't help.

gvegayon on 6 Aug 2019

I have also removed the editor line from bibliography entries for journal articles and attempted to make consistent use of unabbreviated journal names.

@marekborowiec - it would be good if you could also limit the entries in your bibtex file to just those references that you cite in this paper.

arfon on 7 Aug 2019

Done

marekborowiec on 7 Aug 2019

@whedon generate pdf

csoneson on 7 Aug 2019

Attempting PDF compilation. Reticulating splines etc...

whedon on 7 Aug 2019

:point_right: Check article proof :page_facing_up: :point_left:

whedon on 7 Aug 2019

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

csoneson on 7 Aug 2019

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

iimog on 7 Aug 2019

Thanks @iimog!

csoneson on 7 Aug 2019

@whedon assign @iimog as reviewer

csoneson on 7 Aug 2019

OK, the reviewer is @iimog

whedon on 7 Aug 2019

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

marekborowiec on 7 Aug 2019

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 https://github.com/jgm/pandoc/issues/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?

csoneson on 8 Aug 2019

Does that sounds reasonable to everyone?

arfon on 8 Aug 2019

👍2

@whedon start review

iimog on 8 Aug 2019

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

whedon on 8 Aug 2019

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 :))

csoneson on 8 Aug 2019

Thanks @csoneson and sorry for being impatient :)

iimog on 8 Aug 2019

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.

marekborowiec on 8 Aug 2019

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.

gavinmdouglas on 9 Aug 2019

Thank you @gavinmdouglas!

csoneson on 9 Aug 2019

@whedon add @gavinmdouglas as reviewer

csoneson on 9 Aug 2019

OK, @gavinmdouglas is now a reviewer

whedon on 9 Aug 2019

@whedon start review

csoneson on 9 Aug 2019

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1635. Feel free to close this issue now!

whedon on 9 Aug 2019

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