Commit d537a95b authored by peguerin's avatar peguerin
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Update README.md

parent d076c68c
......@@ -71,45 +71,41 @@ The included data files are :
- PYTHON scripts
* `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` : georeferenced sequences alignments by species
#### BASH scripts
* `seq_alnt_filtered_data.sh` : aligns sequences from the same species with MUSCLE and creates coordinates file for each sequence.
* `cluster_freshwater_vs_marine.sh` : according to a list of marine species, moves the fasta and coords files into marine, freshwater repertories.
#### PYTHON scripts
* `fasta_coords_files_species_generator.py` : extracts sequences and associated coordinates from the filtered data.
- BASH scripts
* `seq_alnt_filtered_data.sh` : aligns sequences from the same species with MUSCLE and creates coordinates file for each sequence.
* `cluster_freshwater_vs_marine.sh` : according to a list of marine species, moves the fasta and coords files into marine, freshwater repertories.
#### R scripts
* `equalareacoords.R` : attributes at each sequence an ID of cell of the shapefile of worldmap equal area projection from its coordinates.
* `equalarea_worldcoast.R` : relou
- PYTHON scripts
* `fasta_coords_files_species_generator.py` : extracts sequences and associated coordinates from the filtered data.
### 00-scripts/step3 : filter raw data
======================================
- R scripts
* `equalareacoords.R` : attributes at each sequence an ID of cell of the shapefile of worldmap equal area projection from its coordinates.
* `equalarea_worldcoast.R` : relou
#### 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.
## 3.3 `00-scripts/step3` : filter raw data
### 00-scripts/step4 : Genetic Diversity calculation
====================================================
- 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.
#### R scripts
* `gdval_by_site.R` : removes the cells that are not in the area of at least one marine/freshwater species according to IUCN shapefiles, creates the data files used to generate Figure 1
## 3.4 `00-scripts/step4` : Genetic Diversity calculation
#### JULIA scripts
* `equalarea_numbers.jl` : attributes mean genetic diversity at each equal area grid cell. Genetic diversity is calculated from master data matrices
* `metrics_by_area_and_species.jl`: generates files for statistical analysis at next step : mean genetic diversity per cell, genetic diversity per species per cell, number of individuals per species, number of species per cell, cell coordinates, cell ID...
* `Lib_GD_summary_functions.jl` : functions to calculate genetic diversity at species level and cell level
- R scripts
* `gdval_by_site.R` : removes the cells that are not in the area of at least one marine/freshwater species according to IUCN shapefiles, creates the data files used to generate Figure 1
- JULIA scripts
* `equalarea_numbers.jl` : attributes mean genetic diversity at each equal area grid cell. Genetic diversity is calculated from master data matrices
* `metrics_by_area_and_species.jl`: generates files for statistical analysis at next step : mean genetic diversity per cell, genetic diversity per species per cell, number of individuals per species, number of species per cell, cell coordinates, cell ID...
* `Lib_GD_summary_functions.jl` : functions to calculate genetic diversity at species level and cell level
### 00-scripts/step5 : Statistical analysis
===========================================
#### R scripts
* `model_area_GDval.R`
* `model_species-area_GDval.R`
## 3.5 `00-scripts/step5` : Statistical analysis
- R scripts
* `model_area_GDval.R`
* `model_species-area_GDval.R`
# 4. Reporting bugs
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