update readme in custom_data, and remove entropy from heatmaps

data/custom_analyses_data/README.md

@@ -4,21 +4,26 @@ This subdirectory contains input data used by custom analyses jupyter notebooks
 [theme.py](theme.py): 
 * File for setting custom altair themes, used by all notebooks for plotting
 
-
 [surface_exposure.csv](surface_exposure.csv): 
-* This file contains information about the relative surface exposure of NiV RBP residues.
+* This file contains information about the relative surface exposure of NiV RBP residues
 
 [./alignments](alignments): 
-* ephrin_E2_E3_sequences.fasta Amino acid sequences and alignment of Human and P. alecto EFNB2 and EFNB3
+* **ephrin_E2_E3_sequences.fasta** Amino acid alignment of Human and Pteropus alecto EFNB2 and EFNB3
 * **Nipah_RBP_AA_align.fasta** Alignment of Nipah RBP sequences downloaded from GenBank
 * **wild_type_seq.fasta** wildtype sequence (non codon-optimized) of NiV-M RBP
 * **Nipah-B_MK673572.1.fasta** wildtype sequence of NiV-B RBP
 
+[./alignments/phylo](phylogenetics)
+* **country_genbank_ids.csv** Country of origin of genbank sequences
+* **nipah_whole_genome_alignment.fasta** Alignment of whole genome nipah sequences
+* **nipah_whole_genome_genbank_accession_ids.txt** Accession IDs from genbank
+* **nipah_whole_genome_phylo.tre** Phylogeny of whole genome nipah sequences inferred from IQ-TREE
+
 [./crystal_structures](crystal_structures):
 **PDB files of:**
 * **2vsm.pdb** (Nipah RBP bound to Ephrin-B2)
 * **3d12.pdb** (Nipah RBP bound to Ephrin-B3)
-* **6cmg.pdb** (Hendra RBP bound to mAb m102)
+* **6cmg.pdb** (Hendra RBP bound to mAb m102.3)
 * **6vy4.pdb** (Nipah RBP bound to mAb HENV-32)
 * **6vy5.pdb** (Nipah RBP bound to mAb HENV-26)
 * **7txz.pdb** (Partial Nipah RBP bound to mAb nAH1.3)

data/custom_analyses_data/alignments/phylo/countrydf.csv

@@ -0,0 +1,80 @@
+Accession ID,Country
+NC_002728.1,Malaysia
+OM135495.1,India
+MW535746.1,Thailand
+MK673558.1,Malaysia
+MK673559.1,Malaysia
+MK673560.1,Malaysia
+MK673561.1,Malaysia
+MK673562.1,Malaysia
+MK673563.1,Malaysia
+MK673564.1,Bangladesh
+MK673565.1,Bangladesh
+MK673566.1,Bangladesh
+MK673567.1,Bangladesh
+MK673568.1,Bangladesh
+MK673570.1,Bangladesh
+MK673571.1,Bangladesh
+MK673572.1,Bangladesh
+MK673573.1,Bangladesh
+MK673574.1,Bangladesh
+MK673575.1,Bangladesh
+MK673576.1,Bangladesh
+MK673577.1,Bangladesh
+MK673578.1,Bangladesh
+MK673579.1,Bangladesh
+MK673580.1,Bangladesh
+MK673581.1,Bangladesh
+MK673582.1,Bangladesh
+MK673583.1,Bangladesh
+MK673584.1,Bangladesh
+MK673585.1,Bangladesh
+MK673586.1,Bangladesh
+MK673587.1,Bangladesh
+MK673588.1,Bangladesh
+MK673589.1,Bangladesh
+MK673590.1,Bangladesh
+MK673591.1,Bangladesh
+MK673592.1,Bangladesh
+MN549402.1,India
+MN549403.1,India
+MN549404.1,India
+MN549405.1,India
+MN549406.1,India
+MN549407.1,India
+MN549408.1,India
+MN549409.1,India
+MN549410.1,India
+MN549411.1,India
+MK336155.1,India
+MK336156.1,India
+MK801755.1,Cambodia
+MK575060.1,Bangladesh
+MK575061.1,Bangladesh
+MK575062.1,Bangladesh
+MK575063.1,Bangladesh
+MK575064.1,Bangladesh
+MK575065.1,Bangladesh
+MK575066.1,Bangladesh
+MK575067.1,Bangladesh
+MK575068.1,Bangladesh
+MK575069.1,Bangladesh
+MK575070.1,Bangladesh
+MH523640.1,India
+MH523641.1,India
+MH523642.1,India
+MH396625.1,India
+KY425646.1,Malaysia
+KY425655.1,Malaysia
+JN808857.1,Bangladesh
+JN808863.1,Bangladesh
+JN808864.1,Bangladesh
+FJ513078.1,India
+AY988601.1,Bangladesh
+AJ627196.1,Malaysia
+AJ564621.1,Malaysia
+AJ564622.1,Malaysia
+AJ564623.1,Malaysia
+AY029767.1,Malaysia
+AY029768.1,Malaysia
+AF212302.2,Malaysia