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Gompert lab notes
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Data bases and other resources
growing truncatula
truncatula RILs
Researcher pages
Alex Rego
projects
callosobruchus
Seedle QTL
seedle qtl with new ref
ABC checks
Allele Frequencies
Creating locusids.txt file
DNA Alignment and Variant Calling
DNA Extraction Layout
Estimates of Ne
Exceptional Allele Freq Differences
fastq splitting, parsing, cleaning
Genomic pipeline details
L1-L3 Lines
L11 Allele Freqs, Ne, LD
L14 Selection
LD
lepmap2 LG creation
Phenotypic Data
R/qtl Linkage Map creation
Structure
Structure formatting
Amy Springer
2016 C. mac. inbrd dep vs. lineage, temp, & host
Delta Model
Generalized Linear Model
Presentations
2017 C. mac. admixture adaptation
Methods
Untitled Post
2017 C. tullia & C. haydenii
Lycaeides Fluctuating Selection
2016 Insect Community Raw Data
2017 Insect Community Raw Data
Jacque Pena
Data Analysis
Allele Freqs., He, & Fst
Drought-Irrigation Differences
Genetic Distance
Heterozygosity
POSE Sequence Prep
PSSP Genotype Matrix
PSSP PCA
DNA Extraction Protocol
GBS library prep protocol
Gel Protocol
Plant collection protocol for elevation samples
Quadrant Info
Lauren Lucas
alfalfa 2018
added stakes
BWP eggs from Matt
collected at BST
collected at HWR
collected at JJT
Collected Colias at field plot
fertilizer
field plot planting
field plot soil testing
Field plot watering, summer 2018
field plot: general info
field plot: plans for planting
first meeting with 2018 research team 15 may 18
ladybugs
leaf weight
ordered more plant stakes, etc.
ordered painted lady eggs
painted lady eggs arrived, incubator turned on
permanent plant tags for field plot
photos, developmental stage, penetrometer
plant height
plant phenotyping: leaf area and trichome density
planted field plot
Planting
plants to be housed in BNR and Mari's gh in July
randomizing
slightly rough start to field plot
thinning
thrips biocontrol ideas
to shade cloth or not to shade cloth the greenhouse
Trichome density, round 2
weeding field plot
Alfalfa genome
DNA concentrations
DNA extraction 30vi14
DNA shipped to BGI
Gel 11viii14
Captive Eurycea
captive variance Ne from temporal allele freq. change
coverage captive vs. wild
E. sosorum: de novo assembly
Eurycea sosorum: parsing barcodes
founders information
future predictions
kinship
nana assemblies
nana genest and PCA
nana sam to bam
nana variant calling and h/ theta
new sosorum pca, gst
pooled wild and captive theta and pi
pop allele freq model
SLURM
sosoroum h & theta
sosorum allele frequency and expected het
sosorum de novo assembly con't
sosorum genest and PCA
sosorum reference-based assembly
sosorum sam to bam
sosorum variant calling and theta / h
What the he** is up with the weird nana PCA?!
dessication
Host-plant_preference_June2014
Microbiome_performance_June2014
Spring Endemics Phylogeography
false discovery rate
High FST loci and environmental variables correlations
New theta figure
Stygoparnus ABC
Stygoparnus ABC con't
Stygoparnus ABC con't con't
Stygoparnus lane: remove contaminants from raw sequence reads, parse barcodes
Stygoparnus pairwise Gst
Stygoparnus pairwise Gst con't
Stygoparnus PCA
Stygoparnus reference-based assembly
Stygoparnus variant calling
Stygoparnus: de novo assembly
tests for IBE to compare to IBD
truncatula 2017
All 5 reps worth of caterpillars set up on plants
biocontrol
collection trip #2
first collection trip
for class
Germination
growth chamber settings
How we planted
leaf weight
mapping
ordering supplies
penetrometer, plant pics
plant height
plant phenotyping: trichome density and leaf area, drying leaf
thinning
transplanting
wing pattern mapping
# of QTL as a function of LG size
26v17. added more CSP wings to the dataset
assembly to genome
barcode file
bayesian regression for residuals
BSLMM for each pop
BSLMM for each subgroup
BSLMM going well so far
BSLMM results: breeding values
BSLMM results: pips and effect values
BSLMM results: pve, pge, n_gemma
correlation heat maps with breeding values
entropy to estimate genotypes
finding other genes important to wing pattern
mapping: BSLMM for all inds
Megan will measure two more additional pops.
modularity: position, size, and breeding values
more assemblies; sam to bam
morphoj 23v17
morphoj 24v17
ms
NAs in the size dataset
parsing barcodes
PCA element size
pca with size and position: all inds
pheno correlations (size and position) heat map
Population level: pheno corr
preparing some results for lab meeting 2 June
PVE pop level
raw pheotype data
residuals
scaffolds of interest
split the parsed fastq file by individual
UofU cluster
Variant calling
Variant filtering
which groups and traits have high pips for our scaffolds of interest?
wing pattern drawings
Zach's notes about Lycaeides de novo assemblies
Rozenn
Bayesian Statistics
Part I - 2
Coexistence - Notes
Finding the good plasmid
List of tasks to do
Pando
2019 -12-11 - Pando presentation at the lab meeting
2019-12-02 Filtering vcf files
2019-12-04
2019-12-05 -
2019-12-06 -
2019-12-09
2020 - 01 - 13
2020 - 01 - 14
2020 - 01 - 21
2020 - 01 - 27
2020 - 01 - 28
2020 - 01 - 31
2020 - 01 -29
2020 - 01 -30
2020 - 02 - 03
2020 - 02 - 04
2020 - 03 - 20
2020 - 03 - 30
2020 - 03 -16 - Genetic distances
2020 - 04 - 30
2020 04 09
2020-01-15
2020-01-16
2020-02-10
2020-03-03
2020-03-08
2020-03-10
2020-04-21
2020-04-22
2020-04-23
2020-04-29
2020-05-01
2020-05-06
2020-05-11
2020-05-20
2020-05-22
2020-05-25
20200304
20200305
20200313
Are the small and big trees clustering together?
Are the small and big trees clustering together? - 2
Choosing the references for MuTect2
Downgrading gatk to try other mutect versions
Filter heterozygotes to keep SNPs with >80% hets
Getting familiar with .vcf file
IBD in Pando
IBD in Pando
Labeling heterozygotes
Labeling heterozygotes and finding a good threshold
Last meeting with Zach - plan for the next steps
PC2 score map
PCA - 3
Plot PC1 spatially
Summary of the work from Oct 28th to Nov 21th
Thinking further
This is a test
Untitled
Useful links
Visualization - PCA
Visualization - PCA - 2
Visualize the data - PCA in R
Pando - 2
Analyzing Beast output
ANGSD
ANGSD on Pando data
ANGSD on the cluster
BEAST run 4
BEAST tutorial
Bilan meeting with Zach
Bilan meeting with Zach! July 7th
Calculate effective number of sites!
Coalescent tutorial
Converting Latek to Word
Converting UTMs to Decimal degrees
Filtering - keeping track
Filtering for missing data in friends
Filtering for missing data in friends - 2
Filtering vcf for Friends samples with more than 4 mean read per variant
from vcf to nex
How to make and interpret trees from SNAPP
IBD in filtered friends
Installing BEAST2
Learning more about Beast
Matching coordinates from Karen's file
Message sans titre
Methods!
Moving files to storage folder and making symbolic links
Populus genome size -
Run 1 - Beast
Run 1!
Run 2 - Beast
Run 3 - Beast - my laptop (one run)
Running SNAPP on the cluster - making it work
Scaling the PCA for genetic data
SNAPP - run 8
SNAPP 2 - troubleshooting
SNAPP choice of params!
SNAPP run 9
SNAPP tutorial
Submit a batch job
Tutorial to find the time to the most common recent ancestor
Untitled Post
Untitled Post
What I did today
While waiting to test for convergence of the chains, start a new job (takes time)
Small learnings
About homoplasy
About phasing
Allele/Site Frequency Spectrum - SFS
Bottleneck
Friends
Linkage Disequilibrium
Probability Density Function (PDF)
Probability Density Function (PDF)
Reasoning behind filtering against friends
Samridhi Chaturvedi
cmac RNAseq analysis
path to files
transcriptome_analysis
diapauseExperiment
analysis_October2017
Experiment_2016_overview
MatingExp_JulyAug2017
MatingExperiment_June2016
Notes_Jay/Tyler
fish
barcodes_alignment_variantcalling
Genome Annotation
busco
final_info_extraction
install_repeatmodeler
lepbase
maker
repeatmasker
snp_annotation
Lmelissa_hostAdaptation
adegenet
allele frequency estimates
ancestralStateRecontruction
bayesenv_coop
bayPass
effectssign
experimental comparison
experimental comparison_aug14
Fst calculations
Functional Annotation
manuscript_DRYADscripts
PCA_LDA
popPlant_deets
results
sex-linked
Structural Annotation
treemix
variantCalling_treemix
variantcalling_zgNotes
effectSigns_58
evolution
expResults_enrichmentPlot
getting_enrichments
manhattan plots
parallelism_enrichmentPlot
newresults_aug302017
Lmelissa_microbiome
Microbiome_Lmelissa_Analysis
Lycaeides_hybrids_Dubois
admixture proportions and first pass at plots
aims_proportions
alignment and variant calling
barcodes
clines
common and rare variants
coverage
entropy
filelog_cluster
filtering to get good snps for old and new data
initial runs with popanc
libraryprep
males_analysis
Ncomm_manuscript_revisions
new_scaf_linkagegroup
pairwiseLD
pca_cov_individuals
plink
polarizing_LD
popanc_piecharts
post-entropy
predictability
results
sexchromosome
splitfastq
structural_annotation
temp_annot
ancestry_chromosomes
clines
entropy_hybridindexJHL_plots
males_variant calling
pca
popanc
randomizations
results
revised results predictability
lycaeides_sv
analyses_june2021
matt_transcriptome
filelog_cluster
finalfile
notes for manuscript
reanalyses for missing samples
tophat
transcript_annotation
trim_galore
SRA sequence upload
timema
baypass
climate layers
downloadfiles_SRA
entropy
filelog_cluster
LD
linkagegroups_scaf
phylogeny
sequenceAlignment_variantcalling
snp_annotation
treemix
alignments
analyses
consensus
correlations_randomizationsR
parallelism tests
redoingvariantcalling_bwamem
sam format
standardize_environment_variables
summary_genomespread
top SNPs
variantcalling
bwaalignment_aln
randomization_functions
results
variantcalling
plotsR
Tara Saley
Alfalfa 18
Batch R script
M_trunc_random_forest
breeding_values
Summer 18
Bayesian Analysis- interaction between plant/cat pop
Bayesian Analysis- no interaction
SUMMER 19
Alfalfa_extractions
Libraries
Lyc_Extractions
Lyc_extractions
Zach Gompert
Callosobruchus
C. maculatus genomics of adaptation
Evolutionary dynamics of lentil adaptation
ABC inference of selection
additional abc runs
additional abc runs for revision
additional notes on the C. maculatus Lucigen genome
additional samples and summary
allele frequency change
allele frequency estimates
annotation of C. maculatus genome
C. maculatus, ABC for L14
callobruchus samples
compress and sort alignments
contemporary Ne in seed beetle lines, cont.
DNA extractions for the lentil, mung, and reversion lines
GBS library prep
genome assembly with allpaths-lg, second try
initial test for genetic trade-offs between hosts
linkage disequilibrium
More Ne estimates and plots
Ne estimates
Ne with ETPIs for L1, L2 and L3
new lentil line DNA extractions
new samples
nucelotide diversity
Parsing L14 GBS data
preparing data and genomes for alignment
re-run of exceptional allele frequency differences among lines
recent change in reversion lines
reference-based assembly
results and summary for ABC with different priors
revised figure and anlysis for recent change in reversion lines
samples from Frank in -80
seed beetle PCA
summaries of selection estimates from abc
variant calling
variant filterning, genotype likelihoods
working with sequence data, parse barcodes
Labwork
Eggs/rearing experiments 17-18
Rearing experiments 2017
Sequence log
Wet lab notes
bc1093
cb2020
CHC mapping experiment, rearing and weights
CHC rearing experiment
DNA extractions and library preps; Lycaeides plates 28-35
DNA extractions for 5 Lycaeides genomes with the MagAttract HMW kit
DNA for whole genome sequences, gel image
GBS library prep: alfalfa from Fallon, NV
GBS library preps: C. maculatus new lentil lines
GBS projects, JA14878
Gomp024, NextSeq
Hibernating eggs from 2017 field season
JA15069
JA15243-MiSeq
JA15316
job 13eae1b
job request 113c993=job JA18163
Lycaeides desiccation experiment
Lycaeides DNA extractions and library preps; Lyc-036 and 037
Lycaeides DNA extractions/GBS 2017 focal populations (plus)
New oligos, NGS pure
second round of HMW DNA extractions for whole genome sequencing
Seeds for M. truncatula experiment
Size selection for dimensions samples
Tara's CHC DNA extractions
Trial desiccation experiment
Trial rearing experiments with M. truncatula
Lycaeides
CHCs
Dimension projects
Lmel_Mtrunc_performance
Lycaeides admixture
Lycaeides genome admixture
Lycaeides genomes
Lycaeides host-associated selection
Lycaeides_wing_mapping
Tetons time seires
'survival breeding values' for wild-caught SLA and GLA
3 population admixture test
3 population test continued
a few popanc runs to look at local ancestry blocks within individuals
additional popanc runs with alternative source/reference populations
admixture proportion plot for melissa
alignment and variant calling for pilot data set
alignment of GBS for ancestry inference to melissa genome
alignment of whole genomes to melissa genome, variant calling with GATK's HC
Allele frequencies and variance Ne with Z
Ancestry frequencies with 3 and 7 bp windows for popanc lda
annotations
assembly with platanus
BayAss to detect recent migration in L. melissa
Bayesian isolation-by-distance and isolation-by-population models
Bayesian regression for phenotypic data
breeding values for wild-caught individuals
BSLMM for body size with samtools/GATK union SNPs
CHC variant calling
code for genetic diversity figure
common and rare variants-22viii13
Comparative alignment of the Dovetail L. melissa genome and the older L. melissa genome with linkage map
comparative genome alignment
Comparison of GATK and bcftools variants
Contemporary Ne in L. melissa populations
cross-validation, area under the ROC curve
cross-validation, combined experiments
cross-validation, continued
DA to detect migrants in L. melissa
data from mapping family crosses
density phylogenetic trees
depth across all indiviudals and sites
DNA sequence alignment and variant calling for 2018 CHC data set
Dxy for Lycaeides genomes, correlations, autocorrelations, evidence of hybridization and ancestry blocks
entropy analysis low frequency and rare vars-23viii13
entropy analysis of common variants-23viii13
entropy k = 1-26viii13
entropy results, pca
entropy runs to infer local ancestry frequencies at ancestry informative markers
entropy short chains-22viii13
entropy, population structure and genotypes for melissa
excess Z-linkage of top parallel BayPass SNPs
F4 tests
family posterior cross-validation for adult weight
files rearranged
final Lep-MAP2 linkage map with multiple families
first pass at Sierra Nevada genome done
Formatting data for migration surface analysis
functional annotation for melissa genome top performance SNPs
GBS to melissa genome (draft 0.1)
gemma analyses on dorc
gemma analyses: multiple chains and combined data sets
gemma posterior predictive family cross-validation
gemma results, survival with probit model
gemma, probit posterior predictions
Genetic architecture of caterpillar CHCs, initial results
genetic diversity and LD in the experimental popualtions
genome annotations and tests for enrichment
Genotype estimates and individual-based PCA
Genotype estimates for CHC data with entropy
genotype estimation for rearing experiment individuals
Getting genotype estimates for heritability of body size, gemma
IBD/IBA for natural L. melissa populations
inferring recombination rates, estimating LGs
initial popanc analyses with Z (23) chromosome
L. melissa alignment and variant calling for migration surfaces
L. melissa variant filtering and genotype estimation for migration surfaces
L. melissa/M. truncatula, Gemma runs
linkage maps with Lep-MAP2
locus effects with combined sets
looking for the L. melissa sex chromosomes
lycaeides admixture proportions-29viii13
Lycaeides whole genome phylogenetics with Doevtail reference genome
Lycaeides whole genome phylogenetics with Doevtail reference genome, take 2
Lycaeides whole genome SNP phylogeny
Lycaeides whole genome variant filtering
Lycaeides whole genomes, variant filtering and formatting for phylogenetics
lycaeides, Qmatrix file prep. and analysis
Main ancestry frequency analyses for Lycaeides genome admixture
mapping families, preparing data and alignment
Medicago truncatula hapmap lines
Medicago truncatula SNP data
melissa genome annotation
melissa genome annotation, initial training for ab inition gene prediction
melissa genome functional annotation
melissa, idas, and warner assemblies with allpaths-lg
Mirgation surface analysis and summary
ML allele frequency inference for pilot data set
more mummer runs and results
multi-species comparative genome alignment
Multilocus mapping of CHC in Lycaeides, 2018 data
mummerplot L. warner vs each
New sequence data from core pops and aspen, fastqc, filtering, parsing
Notes for revisions
now trying assembly of L. anna genome
Overview, wing pattern mapping
parsing sequence data from the selection experiment and additional melissa populations
Patterns of allele frequency change
pca on posterior expected genotypes-3ix13
pca with melissa, admixture project populations only
perfromance genetics and genetic variation in GLA and SLA
polygenic modeling of survival and adult weight with gemma
polygenic modelling continued
polygenic modelling, individual and combined experiments
popanc, sex chromosome runs with local ancestry
Population allele frequences for GATK and samtools/bcftools variants/gls
population allele frequencies
posterior cross-validation for adulat weight, results
posterior cross-validation for adult weight
predicting survival, some cool results
prediction for cross-validation
preparing data for entropy analysis
preparing data for wild breeding value estimation
Preparing the Medicago trauncatula data for mapping
Prepping and mapping with body size data
probit model
probit model for survival
processing sequence data
pve in SLA on Ac is similar when using permuted phenotypes
raw sequence data for additional Lycaeides genomes
re-doing enrichment analyses
re-reunning entropy with autosomal SNPs
Redoing whole genome alignments to the dovetail genome
repititve elements for significant enrichemnts
results from mugsy
running bayenv2 for Sam
Second round of variant calling for CHCs with samtools
sequence alignment cont., summary, and compressing
sequence assembly
Sequence data for CHC 2018 project, filtering and parsing
sfs continued
Simulated wing pattern data
single snp linear mixed models
site frequency spectrum
SNP effect correlations
some entropy results with for Lycaeides-2ix13
Some notes on testing for genetic background by gene interactions (epistasis)
sparse effects from the polygenic models
sparse factor analysis-3ix13
spatial autocorrelation of allele frequencies
splitting variants, making gl files, and running entropy
Starting the final push, additional round of variant calling with samtools/bcftools
summaries of popanc results
summaries of single locus linear model results
Summary analyses for wing mapping
Summary of meliss genome stats and structural annotation
summary of mummer run
Summary of popanc AIM results
test runs of popanc with autosomal data
test with sierra, preparing data and trying assembly with allpaths-lg
Teton time series 2013-2017, variant filtering
Tetons time series 2018, genotypes and allele freqs.
Tetons time series, 2013-2017 alignment and variant calling
treemix analysis
treemix jackknife se and p-values
treemix runs from single unrooted ML tree
treemix with pre-determined root
treemix, answer coming soon
treemix, how to calculate PVE by the model (tree plus migration)
treemix, just checking it out
Trees for 1000 bp SNP windows
Variance effective pop. sizes for Lycaeides
Variance effective population size estimates, 2013-2017
Variance Ne with Bayesian allele freq. estimates
Variance Ne with GATK vs. samtools/bcftools
variant calling
variant calling and filtering by family for melissa crosses
variant calling and filtering for Lycaeides ancestry inference
variant calling and vcf
variant calling continued
Variant filtering with Samtools CHC SNPs
visualization of the linkage map
whole genome alignments with mugsy
Z chromosome 1000 SNP trees
Methods
detecting_selection
general computer programs
inference from genetic time series data
mapping&landscapes
additional runs
additional runs, binary measure with linear model
additional simulations and analyses for revision
additional simulations to assess the effect of increased sample size
analysis of human Uygur population with popanc
another popanc run to evalute no. snps for LDA
change to cross-validation procedure for popanc
effect of SNP number for popanc
errors and re-runs
final analyses of simulations for plots
initial summaries and scripts
initial test of population ancestry program
method to infer selection and Ne from genetic time series data
more CV redos
more on cross-validation
new version of popanc
parse mid parcodes
popanc and number of SNPs for LDA, comparison with structure
popanc first round of results for paper
popanc re-runs, bug in model
popanc summaries complete
popanc test run
popanc vs structure
popanc with migration, for revisions
popanc with mouse hybrid zone data
popanc with selection
popanc with selection
popanc, new scale update, test 2
popanc, processing migration simulation results
popmod-program to estimate allele freqs. and genotypes
population ancestry tests continued
preparing new files for popanc
re-run Uygur
re-running popanc with mouse data
redoing CV runs
runs for paper
simulations and analyses with replicated genotypes for Rhagolettis
simulations based on Rhagolettis genetic data
simulations from T. cristinae GBS data
Simulations to evaluate BSLMM for measuring selection
spatpg working, first real test
update to estpost for entropy
Other
alfalfa project
aspen genetics
deme-by-deme model
frog hyrid zone
GrassesGenVar
Ithomine_hybrid_zone
Xip_artificial_hybrids
alfalfa GBS alignment to genome
alfalfa GBS data
alfalfa GBS library information
alfalfa genome sequence data
alfalfa whole genome assembly with ALLPATHS-LG
analyses for Matt's populations
aspen vcf to genotypes
Aspen/Pando, alignment with bwa mem
Aspen/Pando, low number of variants, trouble shooting
assembly of preliminary data for proposal
clustering to count haplotypes as a first pass at ploidy
Data and goals
data for Maria's frog hybrid zone
defining hapltype loci
deme-by-deme "metapopulation" model overview
discriminating between diploids and triploids
entropy runs for Ithomia hybrid zones
extract genotypic data, test run
fallon data, barcode parsing
fallon, alignment, compression, sorting and indexing
fallon, variant calling and fitlering
filtering and combining vcf files
Filtering aspend pando plus rangewide, iteration 1 (pre ploidy calling)
Generating a panel of normals for MuTect2
genomic clines for Maria's frog hybrid zone data
grabbing SNPs for haplotype loci and narrowing the set down
individual-level summaries of genetic variation for the fallon population
new bgc analyses
Overview and allele frequency information
overview and refinement of pipeline
Pando plus variant calling and filtering with samtools/bcftools multiallelic variant caller
Pando plus, estimating allele frequencies and genotypes for the bcftools multiallelic SNPs
parsing take two
PCR duplicates and mutect2, redoing alignments
plans for estimating haplotypes
plans for melissa performance assays across alfalfa populations
Preparing sequence data for and performing de novo clustering/assembly
Processing the pando and rangewide aspen samples
PSSP, reference-based alignment with bwa
Re-doing the PSSP alignments with bwa-mem, and variant calling
removing indels, recreating bam files, and extracting haplotype data
results from initial attempt at haplotype counting
Running MuTect2 w/o the PoN
start project, form for DNA extractions
Summarizing genomic cline analyses
summary of variant calling, 1st pass
Untitled Post
variant calling alfalfa GBS with GATK
variant calling for diploids and triploids
variant calling with GATK
variant comparison for dips and trips
variant filtering and genotype estimation
Xip, filtering variants, ancestry inference and null sims
Timema
dark morph fluctuating selection
Structural variants
Timema curi islands
Timema field experiments
Timema genome
Timema radiation plus
Timema redwood
Timema_diversity
timema_misc
TimemaGeneticArch
'final' dark morph freq. analyes
500 genomes, het. vs. survival correlation
500 Timema genomes, genotype point estimates
ABC demographic inference with non cristinae populations
abc from genome SNPs to infer migration rates
Adding melanic Hwy 154 bugs
additional ABC run for 10 population pairs
additional summaries and plots of temps. affect on dark morph freqs.
aligning new mapping family data
alignment and variant calling for dark morph genomic change
Alignment and variant calling for the 2019 T. chumash experiment GBS data
Alignment and variant calling for whole genome T. cristinae with Dovetail 3
Alignment and variant calling for whole genome T. cristinae with Dovetail 3, take 2
alignment for structural varian paired-end reads
alignment of mapping families to green morph genome
alignment of Moe's Timema genomes
Alignment of T. curi whole genomes to T. curi consensus genome file
alignment, variant calling, and allele frequencies for 2016 cline samples
Alignments of Timema genomes versus melanic version 3
allele freq. and genomic change for 128 and 702.1 in ecology letters experiment
allele freq. and initial analysis of genomic change for FHA
alternative approach to define LG's
analysis of the Timema single generation experiment-21viii13
association between Fst and GWA effects, whole genomes
Bayesian hierarchical model for fluctuating selection on dark morph
Bayesian ridge and lasso, comparison with Bayesian model averaging for T. chumash experiment
bgsr mostly done running
bgsr software, bug fixes-27viii13
bgsr test take two-29viii13
bgsr working? ready to run with Timema data-29viii13
bgsr, new test with simulated data-29viii13
BSLMM analyses for color and survival in T. chumash 2019 experiment
BSLMM analyses for color and survival in T. chumash 2019 experiment-melanistic reference genome
Calculating approximate selection gradients from glm regression coefficients
categorical distance mantel test for IBD within two non-cristinae species
Chumash color mapping CV with and w/o epistasis
cline in stripe frequency across a T. cristinae transect
clines 1996 and 2001 combined
code to show selection candidates
Color locus heterozygosity
Color overlap
Comparative alignment, T. cristinae genome versus Tanja's T. poppensis
Comparative genome alignment of T. cristinae dark vs. green de novo
Comparative genome alignment of T. cristinae green vs. dark morphs
comparative mapping and orientation of LG8 with green genome
comparison of parallel differentiation and bgsr
comparison of predictability for stripe and color at HV
compress, sort, and index Moe's genomes
compressing, sort and index genomes
compressing, sorting and indexing alignments for plates 5 & 6
compressing, sorting and indexing new mapping families
compressing, sorting and indexing sv data
Connecting color-associated SNPs with survival in the Timema chumash 2019 experiment
correlations in order of scaffolds between parents in large family
Coverage from whole genomes Ecol. Letters across scaffold 128
dadi analysis with T. cristinae genomes
dark morph phenotypic and genomic change, list of files
defining mel and stripy based on the dovetail genomes and mapping families
defining the indel
defining the indel, update
delimiting the inversion
Delineating SVs
demographic results
desiccation experiment
Diversity and differentiation between A and C treatment for the OGA between generation experiment
dumb problems
Ecol. Letters GBS, dovetail genome, het fitness
entropy analysis for Santa Barbra T. cristnae
error, re-running alignments, etc.
error, redo
FHA variance Ne
filtering new 500 genome variants
filtering sperm donor variants
filtering SV alignments
final time series (ARMA) analyes for Timema and other data sets
finally some progress with recomb-5ix13
first pass at comparative ordering and oreitnation of LG8
found missing individuals
Fst and HMM for 20 kb windows with Moe's GBS data
fst between morphs for genome data
fst for dsr's in 10 population pairs
fst for revised top pip SNPs
full time seires, stripe frequency over time
GATK-friendly processing continued
GEBVs and G-matrix for Timema color traits
gemma = fail
gemma with GBS data from Ecology Letters
gemma, 500 genomes, BSLMM probit model with maf > 5%
genetic architecture and Fst at the LG level
Genetic differentiation for candidate color genes, chumash vs. podura
genome from Dovetail and new LGs
genomic change for mel in FHA
genomic change for stripy and mel in OGA (science experiment)
genomic change for stripy and mel in the Ecology Letters experiment
genomic change, re-doing alignment and variant calling, plus filtering
genotype and allele frequency estimation
Genotype estimates from lumpy/svtyper
Heterozygosity for SVs
hidden markov model to identify regions of high genetic differentiation
High genetic differentiation regions and allele frequency change in experimental populations
HMM model with N1 and FHA (Doro's populations)
hmm, parameters (partially) estimated from the data
identifying brown contigs in the green morph alignment
Identifying inversions from the mugsy comparative alignment
Identifying inversions from the mugsy comparative alignment, continued
indel realignment
inferring selection for FHA 2011 to 2013 for mel
initial evidence of fluctuating selection on the dark morph
initial gemma analysis with 500 (491) timema genomes
initial pimass results
initial results for bgsr
Intermediate color selection experiment
LD among top color PIP SNPs in chumash
LD between vs. within morhps for high HMM regions
LD for exceptional change SNPs
LD for striped vs. unstriped
linkage groups with the new mapping family data
LMM results and thoughts
MAF x Fst for 20 kb windows in T. cristinae
Mapping color in gemma with epistatic effects from mapit
mapping stripe in timema 500 genomes
merging alignments and assigning ids
merging alignments for plates 5 and 6
merging mapping family alignments and variant calling
Modeling expected fitness in the T. chumash experiment
moe's data minus indel realignment
moe's data, indel realignment with GATK
moe's data, initial problems and indel realignment
moe's data, remove duplicates
more thoughts on gemma analyses
moved some timema sequence and alignment files
mugsy to compare Dovetail and original T. cristinae genomes
new data and alignment: sperm donor and non T. cristinae genomes
new data for the mapping families
new DSR analyses
new fst plots with empirical quantiles and HMM
new T. cristinae analyses, estimating fst
new trait-associated SNP analyses, ecotypes and experiments
NFDS stripe field experiment
No. of QTN in the indel and mel-stripe, 8 of 10 species
Note from Patrik on mapping families
Notes on Timema sp. whole genome alignment and variant calling prior to T. curi project
Null simulations, expected selection gradients for T. chumash
OGA, genomic vs. phenotypic change
overview
overview
parallel divergent change and parallel high genetic differentiation
parallelism based on binary classification of high and normal fst loci
parallelism cont.
parallelism in pi from empirical quantiles.
parallelism or the lack there of in timema
PCA and genotype freqs. for non-T. cristinae species
pcr duplicates
Permutation tests related to the inversion
pi in selection candidates
pimass on experimental genomes to estimate no. snps and pve
pimass, 500 genomes, minimum MAF 5%
pimass, continued
Population genetics of SVs
Population genomic analyses of the sequences in SVs
Population genomic analysis of sequences withing SVs
preparing a genome for GATK
preparing for reference assemblies
problem with scaffold and locus ids for T. cristinae ecotype pairs on genome v0.3
Processing alignments and variant calling for Timema genomes against the melanic version 3 reference
Processing data for T. cristinae clines on HWY 154 (non-Refugio)
processing sperm genome alignments
processing whole genome sequences from the ecology letters experiment
Quantifying host color space filling by Timema
re-doing cristinae analyses; new plan
Re-doing Hwy 154 processing
re-ran and summarized Fst for trait-associated SNPs
re-running abc
re-running alignment and variant calling with the ecology letters GBS data
re-running compression and sorting on 500 genomes
re-running genomic change in FHA and OGA by sub-scaffolds
read group header, more problmes
recalling variants with GATK on the 500 genomes
recomb too high, revised-5ix13
recombination estimates with the merged families
recombination prop. estimates-4ix13
recombination rate test with HMM defined region
reference assemblies, plates 5 and 6
region pips
removing PCR duplicates
rerunning the T. crisinae 500 genome alignments again
results from dark morphs fluct. selection analyses
Revised figures and code for the new indel focused Timema paper
revisions for within generation transplant experiment, Aaron's trait associated snps
sanity check on timema 500 genomes
scaffold 128 & 702.1 change controlling for diversity in OGA science experiment
scaffold 128 - left has more change than expected for diversity
Searching for the deleted color locus in the green and stripe genomes
Second (2019) T. chumash experiment, selection gradient analysis
Second dovetail assembly
Selection for Ecology Letters (FHA 2011) bugs with six genotype model
Selection in FHA based on six genotype model
selection on adenostoma
Sequence data, 2019 redwood experiment plus
sex chromosomes (or the lack thereof)
sex chromsome search, take 2
size of HMM regions continued
size of HMM regions in bp
SNP-based analyses for Timema genome paper revision
some final summaries for prediction manuscript
sperm segregation distortion
sperm sequence data and alignment
splitting fastq files
splitting scaffold 702 and creating genome version 1.3
stripe != survival
stripe time series analysis
stripe-associated SNPs and allele frequency change, within-generation transplant experiment
Summary from Patrik, getting at evolution of color genetic arch.
summary of Bayesian analyses of dark morph frequency as of Sept. 25th
summary of HMM three-state model results
summary of variant calling with bulk samples
SV project, results/SVs from Kay Lucek
T. chumash 2019 GBS, realignment and varianct call with melanic genome
T. chumash gemma preliminary results with stripe genome
T. chumash, selection gradients on GEBVs
T. cristinae llinkage map with LM2 and 2nd Dovetail assembly
T. cristinae sex chromsome, depth and Dovetail
T. curi project, and creating the consensus sequence
T. curi, variant filtering and allele frequency inference
T. knulli, mapping performance on RW versus C
T. knulli, mapping performance on RW versus C: initial results and PCA by LG
T. knulli, mapping weight change on redwood and Ceanothus
T. petita and knulli genotype estimates for performance mapping
Test for epistasis affecting color in chumash with MAPIT
the significant SNP
timema 500 genomes, extracting genotype likelihoods
timema bgsr analysis running on rc-29viii13
timema bgsr take three-4ix13
timema bgsr, take two-2ix13
Timema cristinae Dovetail genome 2 linkage map
timema genome clustering by linkage groups version 0
timema genome v 0.2
timema genomes LMM
timema genomes, gemma probit model
timema genomes, gemma results and next attemps
timema linkage groups
timema linkage groups continued
timema radiation genomes, 20kb windows and parallelism
timema radiation genomes, EM allele frequency estimation and Fst
Timema radiation, Fst and HMM
timema radiation, genomic autcorrelation
Timema radiation, initial HMM results
timema radiation, variant filtering and genotype likelihood estimation
timema revisions, non-parallel divergence SNPs for enrichment
timema whole genome Fst
timema whole genome Fst, parallelism
Timema, number of color QTL/QTN based on lateral color
trait-associated SNP analyses based on HMM regions
uneveness of data, skewed 'allele freqs', bulk samples
Updated selection estimates for FHA with Mel-Stripe
variant calling continued
variant calling for additional whole genomes that were part of the sperm donor run
variant calling for merged mapping families
variant calling for sperm data
variant calling natural populations, step 1
Variant calling of T. curi genomes agains chumash consensus
variant calling with GATK unified genotyper
variant calling, step 2
variant calling, within generation experiment whole genome sequences
variant filtering 500 genomes
Variant filtering and genotype estimation for T. cristinae to identify green homozygote
variant filtering and genotype estimation for within generation whole genome sequences
Variant filtering and genotype inference with Timema chumash 2019 experiment
Variant filtering and genotype inference with Timema chumash 2019 experiment--melanistic reference genome
variants for 84 Timema sp. genomes for phylogenetics
visualization of comparative alignments, orientation of scaffolds
Visualizing the chumash fitness landscape with igraph
whole genome alignment and variant calling ecol. letters experiment, dovetail 3
whole genome alignment original T. cristinae genome vs. dovetail 2
working linkage groups
~100 pimass runs, almost there
Zach Valois
P. boreus parallel evolution
Citations - Ecological Speciation
Citations - General
Citations - methodology/concepts
Citations - scorpion taxonomy/systematics
Lab protocol
Methods: quantifying color
Paruroctonus sp nov/revis
Vachoni Phylogeography
Molecular data
Standard operating procedures
Alignment and variant calling
autoclave-dry
For autoclaving dry supplies: tips, tubes, etc.
autoclave-liquid
For autoclaving liquids (nutrient agar, etc.)
Gels
potassium buffered saline
SLURM
Taking care of eggs
UNIX commands
UT GSAF
What we are reading
Amy
Lab Meeting
Tara
Zach
Gompert lab notes
Citations - methodology/concepts
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