README.txt
----------

This README file describes the contents of the data files provided as part of the study "Spatiotemporal dynamics of giant viruses within a deep freshwater lake reveal a distinct dark-water community".

Files and Directories:

1. LBGVMAG_nucl.tar.gz
   - Content: Nucleotide sequences of LBGVMAGs generated in this study.

2. LBGVMAG_prot.tar.gz
   - Content: Protein sequences of LBGVMAGs generated in this study.

3. phylogenetic_trees_alignments.tar.gz
   - Content: Contains all alignment and phylogenetic tree files listed below.
   - Subcontents:
     - Mirusvirus_heliorhodopsin.aln: Alignment file for Heliorhodopsin sequences from mirusviruses and reference sequences from RefSeq database.
     - Mirusviurs_Heliorhodopsin.treefile: Phylogenetic tree file for Heliorhodopsin from mirusviruses and reference sequences from RefSeq database.
     - Mirusvirus_MCP.aln: Alignment file for the Major Capsid Protein (MCP) sequences of freshwater mirusviruses, marine mirusviruses, and endogenous mirusviruses.
     - Mirusvirus_MCP.treefile: Phylogenetic tree file for the Major Capsid Protein (MCP) of freshwater mirusviruses, marine mirusviruses, and endogenous mirusviruses.
     - nucleocytoviruses_7marker_concat.aln: Concatenated alignment of 7 marker genes from nucleocytoviruses and reference GV genomes.
     - nucleocytoviruses_7marker_concat.treefile: Phylogenetic tree of the concatenated 7 marker genes from nucleocytoviruses and reference GV genomes.

4. Contigs.tar.gz
   - Content: Contigs assembled by Flye v2.8 and polished using both long and short reads in the original publication (DOI: 10.1128/msystems.00433-22), which was used for recruiting single-contig GV MAGs in this study.