Cell - 8 September 2016

Continued

REAGENT or RESOURCE SOURCE IDENTIFIER
SPRI works HT Beckman Coulter Cat#B06938

Deposited Data

De novo assembly DDBJ/ENA/GenBank BioProject PRJNA323691

Experimental Models: Organisms/Strains
See Table S1for list of strains sequenced This paper N/A

Sequence-Based Reagents
FDC1-W497-FW: 5^0 -TGCAGATCAGATGGC
TTTTG-3^0

This study N/A

FDC1-W497-RV-STOP: 5^0 -GCAATTATTTATA
TCCGTACCTTTTT-3^0

This study N/A

FDC1-W497-RV-ALT: 5^0 -GCAATTATTTATATC
CGTACCTTTTC-3^0

This study N/A

Delta12: 5^0 -TCAACAATGGAATCCCAAC-3^0 Legras and Karst, 2003 N/A
Delta21: 5^0 -CATCTTAACACCGTATATGA-3^0 Legras and Karst, 2003 N/A

P86: 5^0 -ACTCCACTTCAAGTAAGAGTT-3^0 Huxley et al., 1990 N/A
P87: 5^0 -GCACGGAATATGGGACATACTT-3^0 Huxley et al., 1990 N/A
P88: 5^0 -AGTCACATCAAGATGGTTTAT-3^0 Huxley et al., 1990 N/A

Software and Algorithms
Agilent Chemstation software Agilent Technologies, USA https://www.agilent.com/en-us/products/
software-informatics/massspec-workstations/
gc-msd-chemstation-software
AUGUSTUS (v2.5) Stanke and Morgenstern 2005 http://bioinf.uni-greifswald.de/augustus/; RRID:
SCR_008417/
BEAST (v1.8.2) Drummond et al., 2012 http://beast.bio.ed.ac.uk/; RRID: SCR_010228

Burrows-Wheeler Aligner (BWA) (v0.6.1) Li and Durbin, 2009 http://bio-bwa.sourceforge.net/; RRID: SCR_010910
CD-HIT (v4.6) Fu et al., 2012 http://weizhongli-lab.org/cd-hit/; RRID: SCR_007105
ExaML (v3) Kozlov et al., 2015 http://sco.h-its.org/exelixis/web/software/examl/
index.html

FASconCAT (v1.0) Ku ̈ck and Meusemann, 2010 https://www.zfmk.de/en/research/
research-centres-and-groups/fasconcat
fastStructure (v1.0) Raj et al., 2014 https://rajanil.github.io/fastStructure/
FigTree (v1.4.2) http://tree.bio.ed.ac.uk/software/figtree/; RRID:
SCR_008515

Gene-E Broad Institute http://www.broadinstitute.org/cancer/software/
GENE-E/
Genome Analysis Toolkit (GATK) (v2.7.2) Broad Institute,McKenna et al., 2010 https://www.broadinstitute.org/gatk/; RRID:
SCR_001876
Idba_ud (v1.1.1) Peng et al., 2010 http://i.cs.hku.hk/alse/hkubrg/projects/idba_ud/

liftOver Kuhn et al., 2007 http://genomewiki.ucsc.edu/index.php/
Minimal_Steps_For_LiftOver
LogCombiner Drummond et al., 2012 http://beast.bio.ed.ac.uk/logcombiner
MACSE (v1.01b) Ranwez et al., 2011 http://bioweb.supagro.inra.fr/macse/index.php?
menu=intro&option=intro
MAFFT (v7.187) Katoh and Standley, 2013 http://mafft.cbrc.jp/alignment/software/; RRID:
SCR_011811

Musket Liu et al., 2013 http://musket.sourceforge.net/homepage.htm#latest
PAL2NAL (v14) Suyama et al., 2006 http://www.bork.embl.de/pal2nal/
PartitionFinder (v1.1.1) Lanfear et al., 2012 http://www.robertlanfear.com/partitionfinder/

Picard Tools (v1.56) Broad Institute http://broadinstitute.github.io/picard/; RRID:
SCR_006525
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e2 Cell 166 , 1397–1410.e1–e10, September 8, 2016