Hey I'm new here, and pretty new to R as well.
I am trying to perform a PairwiseAlignment on 25 protein sequences from Uniprot.
I have 25 Fasta files in this format:

    >tr|A0A287AI92|A0A287AI92_PIG Carbonic anhydrase 1 OS=Sus scrofa OX=9823 GN=CA1 PE=1 SV=1MTSPAWGYDGEYGPEHWSKVYPIANGNNQSPIDIKTSETKHDTSLKPISV.....
I loaded the Fasta files to R using :

    ProtSeq_1 <- read.fasta("C:/Users/tiriy/Documents/A0A287AI92.fasta")
Now I'm trying to order the Fasta files into data frame - which I miserably failed at doing and looping the Pairwise alignment with for loop like so:

    comb<- combn(10,2)
    MT1 <- a_data_frame
        for (i in 1:ncol(comb)) {
          x<-pairwiseAlignment( toString( MT1 [comb [1,i],1]),
         toString(MT1 [comb[2,i],1]),
        substitutionMatrix = "BLOSUM100", 
        gapOpening = -2, 
        gapExtension = -8, 
        scoreOnly = FALSE)
          fileA<-paste0("C:/Users/uri/Desktop/", i,"-","blusom",".txt")
          writePairwiseAlignments(x,file=fileA)}

- How can I data frame all the sequences?
- Or otherwise any other suggestion on looping the pairwise alignment on these fasta files?

Many thanks in advance! 
I hope I'd be able to give my aid back in the future
So since I was able to solve all my problems alone, I thought it would be helpful if I posted my script here for future reference.
(Note the final product is a data frame for all combinations of sequences pairwise alignments with sequence descriptions for both subject and pattern and their scores)

    # Installing and loading packages pairwise alignment blosum50 and blosum100 ----
    
    # Installing seqinR R package:
    install.packages("seqinr")
    # seqinR end
    
    # Installing Bioconductor - Biostrings
    chooseCRANmirror() # Getting inside CRAN mirrors
    1 
    # Choosing the first option
    install.packages("BiocManager") # Installing BiocManager in order to install Biostrings
    BiocManager::install("Biostrings") # Installing Biostrings via BiocManager
    # End of Biostrings installation: Biostrings, BiocManager
    
    # seqinr:
    require(seqinr)
    # seqinr end
    
    # Biostrings:
    require(Biostrings) # Loading Biostrings into library
    #Biostrings end


    # Step 1 - Listing all fasta files:----
    all_fasta<-list.files("C:/Users/tiriy/Desktop/TheProject/ProjectR/fastas") 
    # Making a vector to reffer to all fasta files in certain folder
    # End of step 1

    # Step 2 - Making a data frame out of the files ----
    # using biostrings package - readAAStringSet
    # And converting it into a dataframe:
    A <- readAAStringSet(all_fasta) #Reading all fasta files at once {biostrings}
    A1 <- names(A) # Setting vector to hold all the names from the fasta 
    # files retrievd in vector A
    A2 <- paste(A) # Setting a vector A2 with pasted values from vector A
    ProtDF <- data.frame(A1,A2) # Using A1 as first olumn and A2 as second column
    # End of step 2 

    # Step 3 making a generation of combinations for pairwise alignment ----
    D <- combn(25,2)
    # End of easy peasy step 3

    # Step 4 loading data:---- 
    # 
    # Loading Data:
    data("BLOSUM50")
    data("BLOSUM100")
    # End of step 4

    # Step 5 - assigning empty vectors for a for loop----
    ScoreX <- c()
    nameSeq1 <- c()
    nameSeq2 <- c()
    # End of step 5

    # Step 6 THE LOOP ----
    for (i in 1:300) { 
        dumpme<-pairwiseAlignment(toString(ProtDF[D[1,i],2]) # combining all pairwise alignment possible
                                  ,toString(ProtDF[D[2,i],2]), # for 25 sequences = 300 combinations
                                  substitutionMatrix = "BLOSUM50", # pairwise alignment settings
                                  gapOpening = -2,
                                  gapExtension = -8,
                                  scoreOnly=FALSE)
       # filling vectors
      ScoreX[i]<-c(dumpme@score)   #score
      nameSeq1[i]<-c(as.character(ProtDF[D[1,i],1]))
      nameSeq2[i]<-c(as.character(ProtDF[D[2,i],1]))
      
    }
    #End of step 6 

    # Step 7 creating a dataframe ----
    BLOSUM50DF<- data.frame(nameSeq1,nameSeq2,ScoreX ) # DF consists of columns sequence 1 and 2 names as writen in fasta
    colnames(BLOSUM50DF)<-c("Sequence 1","Sequence 2","Score") # score achieved in pairwise alignment calculation
    write.csv(BLOSUM50DF,file="C:/Users/tiriy/Desktop/TheProject/BLOSUM50DF.csv") # writing to file (csv)
    # End of step 7

