Commit 2dd7d739 authored by peguerin's avatar peguerin
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Update README.md

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# 3. Scripts Code Source
## 3.1 `00-scripts/step1` : filter raw data
## 3.1 [00-scripts/step1](00-scripts/step1) : filter raw data
- BASH scripts
* [filter_raw_data.sh](00-scripts/step1/filter_raw_data.sh) : Keep only the CO1 sequences with lat/lon information
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- PYTHON scripts
* [lat_long_DMS_DD_converter.py](00-scripts/step1/lat_long_DMS_DD_converter.py) : Converts from DMS format to DD format the given coordinates.
## 3.2 `00-scripts/step2` : georeferenced sequences alignments by species
## 3.2 [00-scripts/step2](00-scripts/step2) : georeferenced sequences alignments by species
- BASH scripts
* [seq_alnt_filtered_data.sh](00-scripts/step2/seq_alnt_filtered_data.sh) : aligns sequences from the same species with MUSCLE and creates coordinates file for each sequence.
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- R scripts
* [equalareacoords.R](00-scripts/step2/equalareacoords.R) : attributes at each sequence an ID of cell of the shapefile of worldmap equal area projection from its coordinates.
* [equalarea_worldcoast.R](00-scripts/step2/equalarea_worldcoast.R) : PAS ENCORE DECRIT !!!
## 3.3 `00-scripts/step3` : filter raw data
## 3.3 [00-scripts/step3](00-scripts/step3) : filter raw data
- JULIA scripts
* `Lib_Compare_Pairwise.jl` : functions to compute the Genetic Diversity value from a set of sequences.
* `Lib_Create_Master_Matrices.jl` : functions to create master data matrices that are used to compute genetic diversity.
* `master_matrices.jl` : generates master data matrices from species sequences alignments.
* [Lib_Compare_Pairwise.jl](00-scripts/step3/Lib_Compare_Pairwise.jl) : functions to compute the Genetic Diversity value from a set of sequences.
* [Lib_Create_Master_Matrices.jl](00-scripts/step3/Lib_Create_Master_Matrices.jl) : functions to create master data matrices that are used to compute genetic diversity.
* [master_matrices.jl](00-scripts/step3/master_matrices.jl) : generates master data matrices from species sequences alignments.
## 3.4 `00-scripts/step4` : Genetic Diversity calculation
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