add PNAS_core_code

[ijampei]

Dear Rob,
I would like to add several "core codes" used in the present study (Ito et. al., 2019, PNAS.).
In the directory "PNAS_core_code", there are four sub-directories, categorized by the topics.
Could you please confirm these?

Best regards,
Jumpei

[robjgiff]

Hi there - looks good I merged your changes into the main branch. -r

…

On 12 Nov 2019, at 02:01, Jumpei Ito ***@***.***> wrote: Dear Rob, I would like to add several "core codes" used in the present study (Ito et. al., 2019, PNAS.). In the directory "PNAS_core_code", there are four sub-directories, categorized by the topics. Could you please confirm these? Best regards, Jumpei You can view, comment on, or merge this pull request online at: #1 <#1> Commit Summary add PNAS_core_code File Changes A PNAS_core_code/code_related_to_Genome_screeing/README.md <https://github.com/giffordlabcvr/A3-Evolution/pull/1/files#diff-0> (12) A PNAS_core_code/code_related_to_Genome_screeing/batch_demo.sh <https://github.com/giffordlabcvr/A3-Evolution/pull/1/files#diff-1> (15) APNAS_core_code/code_related_to_Genome_screeing/demo_data/original_MSA.fas <https://github.com/giffordlabcvr/A3-Evolution/pull/1/files#diff-2> (22928) A PNAS_core_code/code_related_to_Genome_screeing/demo_data/tree_first.nwk <https://github.com/giffordlabcvr/A3-Evolution/pull/1/files#diff-3>(1) A PNAS_core_code/code_related_to_Genome_screeing/remove_outlierOTUs.py <https://github.com/giffordlabcvr/A3-Evolution/pull/1/files#diff-4>(91) A PNAS_core_code/code_related_to_Genome_screeing/select_alignment_site.py <https://github.com/giffordlabcvr/A3-Evolution/pull/1/files#diff-5>(75) A PNAS_core_code/code_related_to_Mutation_strand_bias_analysis/.Rapp.history <https://github.com/giffordlabcvr/A3-Evolution/pull/1/files#diff-6>(0) A PNAS_core_code/code_related_to_Mutation_strand_bias_analysis/README.md <https://github.com/giffordlabcvr/A3-Evolution/pull/1/files#diff-7>(13) APNAS_core_code/code_related_to_Mutation_strand_bias_analysis/batch_demo.sh <https://github.com/giffordlabcvr/A3-Evolution/pull/1/files#diff-8>(20) APNAS_core_code/code_related_to_Mutation_strand_bias_analysis/calc_mut_rate_family-level.R <https://github.com/giffordlabcvr/A3-Evolution/pull/1/files#diff-9> (100) APNAS_core_code/code_related_to_Mutation_strand_bias_analysis/demo_data/hg19.fa.head_50000.align <https://github.com/giffordlabcvr/A3-Evolution/pull/1/files#diff-10> (500000) APNAS_core_code/code_related_to_Mutation_strand_bias_analysis/detect_mutations_in_each_TE_integrant.py <https://github.com/giffordlabcvr/A3-Evolution/pull/1/files#diff-11> (165) 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