Ancestral Lighting: Sequences input and output

SEED_BetaBarrel_FPs.fasta: Sequences of fluorescencent proteins (FPs) with desirable features used as a seed to look for a bigger data set.

SEED_BetaBarrel_FP_Maffted.fas: Aligned SEED sequences using MAFFT with the command "mafft --reorder --maxiterate 0 --globalpair input". From this file, a Hidden Markov Model (HMM) can be generated using tools like HMMER (http://hmmer.org/). The HMM can then be used to look for sequences that satisfy it out of an expanded database, like UniREF100. In this casem, the UniRef100 used was version available by August 3rd, 2022 at https://www.uniprot.org/uniref

final_pasted.fas: Sequence Alignment of the best matches to the HMM after filtering by 90% redundancy and minimal sequence length of 200 residues. The filtering was done with CD-HIT (https://bioinformatics.org/cd-hit/).

AC_tree_structure_wASR.txt: Text/Graphic version of the ANCESCON output from the MPI-Toolkit (https://toolkit.tuebingen.mpg.de/tools/ancescon) after using final_pasted.fas as input. The nodes of this tree represent the ancestral proteins.