Supplemental files and data to accompany the manuscript:
Westfall et al. A chromosome-level genome assembly for the Eastern Fence Lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology
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File Name: BUSCO_DW.sh
Description: The script used to run the BUSCO analysis.
MD5 value: 6e7945480e7899ed7bc9de96e6051cd0

File Name: BUSCO_results_Sceloporus_undulatus24.genome_full_table.tsv
Description: Full BUSCO results table for the Sceloporus_undulatus24.genome. Corresponding to Figure 2C
MD5 value: bb8bdc21868ff5bd443adb7ee9bc79fd

File Name: BUSCO_results_Sceloporus_undulatus24.proteins_full_table.tsv
Description: Full BUSCO results table for the predicted proteins from the annotated Sceloporus_undulatus24.genome. Corresponding to Figure 2D
MD5 value: 87eeab27a607fd61652ea8f84323eef8

File Name: Funannotate_DW.sh
Description: The script used to run the Funannotate analysis.
MD5 value: 06f22ff9b53870333f60cacdcc123816

File Name: GenomeAssemblies_34Sceloporus.tar.gz
Description: A tar folder containing the 34 reference-based assemblies (.fasta files) for the 34 Sceloporus species.MD5 value: 
MD5 value: 683b22ac18ae18f2f948097f11e7f488

File Name: GenomeAssembly_HiRise_Sceloporus_undulatus.fasta.gz
Description: A gzipped .fasta file containing the HiRise assembly of the 10X Genomics Chromium data and the Hi-C library prep Illumina sequencing data.
MD5 value: 4c16d8df67d04c997f627d563051cd31

File Name: GenomeAssembly_SceUnd1.0_PBJELLY.fasta.gz
Description: A gzipped .fasta file containing the PBJelly Assembly (SceUnd1.0) of the 10X Genomics Chromium data, the Hi-C data, and PacBio sequencing data. 
MD5 value: f6927247dc794cf8d3acf8be88402282

File name: GenomeAssembly_SuperNova_Sceloporus_undulatus_pseudohap.fasta.gz
Description: A gzipped .fasta file containing the SuperNova Assembly of the 10X Genomics Chromium library prep and Illumina sequencing data.
MD5 value: 976495a30bc07361a8b61e0b558fe270

File Name: MitoGenomeAssembly_Sceloporus_undulatus_Annotation.gff 
Description: A gff file containing the annotation of the mitochondrial genome assembly MitoGenomeAssembly_Sceloporus_undulatus.fasta 
MD5 value: f44c89b51c11ed0b8f7df5953010edbb

File Name: MitoGenomeAssembly_Sceloporus_undulatus.fasta 
Description: A fasta file containing the Sceloporus undulatus mitochondrial genome assembled from the liver RNAseq data from Simpson et al.
MD5 value: cb81aba205aec06f1bbb7cdedd1ec654

File Name: mkgenome_AW-AC.sh
Description: The script used to generate consensus sequences for the reference-based assemblies for each of the 34 other Sceloporus species.
MD5 value: aed67c6a1a6eedef27c02b5aa9fe6279

File Name: Names_SceUnd1.0_PBJELLY_TO_funannotate.txt
Description: A table that matches the original scaffold names from the original PBJELLY assembly to the output scaffold names from the Funannotated PBJelly Assembly, including the SceUnd1.0_top24.fasta for which we provide annotation.
MD5 value: 7d081d7d8a038130f06671f5329de465

File Name: NucleotideAlignment_SceloporusIGF1_FigureS4.phy
Description: A multiple-sequence alignment of the coding region of IGF1 across the sceloporus species. Corresponding to Supplemental Figure S4.
MD5 value: 657f71cef929e32aa95d814a341419f2

File Name RepeatMasker.zip
Description: A folder containing the output from the RepeatMasker Analysis, including a gff file that contains the annotation for the repeat regions.
MD5 value: daa6a744780414f97830e4fa0a53afbf

File Name: SceUnd1.0_top24.annotations.txt
Description: A text file containing the annotations to output from Funannotate.
MD5 value: 10da9bbcda74a59a0cf9109d9ee39bbc

File Name: SceUnd1.0_top24.fasta.gz
Description: A fasta file containing the truncated genome assembly used for annotation pipeline. This file contains only the longest 24 scaffolds (named 1-24 from longest to shortest) from the PBJelly Assembly (SceUnd1.0).
MD5 value: 71fd4bf225cdf2aad5228d711969d26a

File Name: SceUnd1.0_top24.gff3
Description: A gff3 file containing the annotation output from Funannotate for the truncated assembly SceUnd1.0_top24.fasta.
MD5 value: 5447923889a9cc59fc1f12b3f1b7f479

File Name: SceUnd1.0_top24.proteins.fa
Description: A fasta file containing the predicted proteins output from Funannotate for the truncated assembly SceUnd1.0_top24.fasta.
MD5 value: 8d3c16b7fd3d2c38dfc12e42cd3cf271

File Name: SceUnd1.0_top24.transcripts.fa
Description: A fasta file containing the predicted transcripts output from Funannotate for the truncated assembly SceUnd1.0_top24.fasta.
MD5 value: a9f77146ccda704afb457534605d6564

File Name: SceUnd1.0_top24.proteins.fa.report_EnsemblCombined.top.txt
Description: A text file containing the names of the predicted proteins output from Funannotate with their top BLAST hits to ENSEMBL.
MD5 value: 98c70cc5286bd9543b9e762848add091

File Name: TranscriptomeAssembly_Tissues-Embryo_Transdecoder.gff3
Description: A gff3 file containing the annotation for transcriptome assembly, from Transdecoder
MD5 value: c2dc27e419ecfadf36ac0f59c02f97f7

File Name: TranscriptomeAssembly_Tissues-Embryo_Trinity.fasta
Description: A .fasta file containing the Tissue-Embryo Transcriptome output from Trinity.

File Name: TreeFile_Sceloporus_Figure4A.newick
Description: The tree file for making the phylogenetic tree in Figure 4A
MD5 value: 1c590c7a912394b0025693c5fdba7247