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Code contributing to Hodgins KA, Bock DG, Hahn MA et al. (2015) Comparative genomics in the Asteraceae reveals little evidence for parallel evolutionary change in invasive taxa. Molecular Ecology, 24, 2226–2240.
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AssemblyList_June25.txt
AssemblyList_Nov29 - AssemblyList_Nov29.csv.csv
AssemblyList_Nov29 - AssemblyList_Nov29.csv.tsv
CGP EST LIBRARY INFO.txt
CGP_Comp_EST_assembly_info.txt
GISDclassification_species.txt
GISDclassification_species_1.xlsx
InvSyn_speciestree.pdf
InvSyn_speciestree.png
InvasionSyndicate.Rproj
RAxML_species_tree
RAxML_species_tree_rooted
README.md
Seq_info_sunflr.txt
Seq_info_sunflr_relatives.txt
SpeciesSummary.txt
SpeciesSummary_syn.txt
SpeciesTraits_bigtable.xlsx
TraitScore_DistScore.txt
Trait_Finder.R
USinv_family.txt
USinvlist.txt
WeedScore.R
allAstersWeedStatus_20140909.txt
classification_species.csv
classification_species.txt
eol_daisie_species.txt
eol_gisd_species.txt
eol_gris_species.txt
eol_i3n_species.txt
eol_isc_species.txt
getting_traits.R
inv.syndicate.R
is.invasive.func.R
ortho_group10025_cds.prank.best.fas
ortho_group10025_utr3.prank.best.fas
ortho_group10025_utr5.prank.best.fas
ortho_group10037_cds.prank.best.fas
ortho_group10037_utr3.prank.best.fas
ortho_group10037_utr5.prank.best.fas
phylo_plot.png
sample_phylo_trees.R
specieslist.txt
weedtree.png

README.md

InvasionSyndicate

Code contributing to Hodgins KA, Bock DG, Hahn MA et al. (2015) Comparative genomics in the Asteraceae reveals little evidence for parallel evolutionary change in invasive taxa. Molecular Ecology, 24, 2226–2240.

R code by KGT largely used for the purpose of classifying ~40 species included in comparative genomics dataset, using the taxize package in R. Additional work (not described in paper) addresses traits, synonyms, and phylogenies of those species. Main action included in inv.syndicate.R - producing species lists, querying databases, producing trees.

Other R files (not included in paper): WeedScore.R - checking for correlation between "trait score" and distribution. getting_traits.R - combining trait data with sequence data. sample_phylo_trees.R - messing around with plot.phylo() Trait_Finder.R - scraping trait data from USDA PLANTS database (by R. Colautti). is.invasive.func.R - other functions for determining invasion status

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