Phylogenomics of _Paramikrocytos canceri

# Phylogenomics of _Paramikrocytos canceri_

In this repository, the files used for generating a tree of Rhizaria including _Paramikrocytos canceri_ can be

found. The dataset is based on work by Schön et al. (2021) and references therein (full reference in our manuscript).

**1_unaligned_sequences**: contains amino acid sequences of Rhizaria plus outgroups in unaligned fasta format. Regions with 

dubious alignments in sequences from the outgroups were masked by Schön et al. (2021).

**2_merged_alignments**: sequences from directory 1 were aligned using MAFFT v. 7.310, E-INS-I. Following alignment,

sequences from the same species were merged using this script:

https://github.com/markhilt/genome_analysis_tools/blob/master/merge_transcripts.py

**3_gene_trees**: gene trees were constructed from the alignments in directory 2. For this purpose, IQ-TREE2 v. 2.2.0.3

was used, with ModelFinder to test the best-fit model for each alignment.

**4_trimmed_alignments**: before concatenation of alignments for full phylogenomic analysis, alignments in directory 2 

were trimmed with trimAl v. 1.2, using the -gappyout parameter. Trimmed alignments are found in this directory.