Figure 4.2: CBCDetect calculates compensatory base changes in all against all of the aligned sequences. If a multiple alignment is used, the output is a count matrix (uncorrected p-distances), that now can be used as input for PHYLIP, or BIONJ.
The input of CBCDetect is a part of the output from RNAforester or a part of the output from MARNA to be put in by copy & paste:
From RNAforester you get (only pairwise alignments) in the following format:
> Name1 and > Name2 global alignment score:17 ((((...)))) ((((...)))) augcuuugcau augggggccauFrom MARNA you get (pairwise or multiple alignments) in the following format:
AB013372 GCGCCCG-UAGCUCA-A-----UU--GG-------A-UAGAGCG---UUUGA-C-UACGGAUCAAAAGGUUAGGGGUUCGA---CUCCUCUCGGGCGCG AB013373 GCGGAAG-UAGUUCA-G------U--GG-------U--AGAACA---CCACCUU-GCCAA-GGUGGGGGUCGCGGGUUCGAA-UCCCGU--CUUCCGCU AE000930 -GGCCCG-UAGCUCAGA-----CU--GG-------G--AGAGCG---CCGCCCUUGC-A-AGGCGGAGGCCCCGGGUUCAAA-UCCCGG-U-GGGUCCA AB067577 GGGCUAU-UAGCUCA-G-----GU--GG-------U-UAGAGCG---CACCCCU-GAUAA-GGGUGAGGUCCCUGGUUC-AAGUCCAGG--AUGGCCCA AF034440 GUUGAUG-UAGCUUA-A-----CC--C-----------AAAGCA---AGGCACU-GAAAA-UGCCUAGAU-GAGU-CUCCCA---ACUC--CAUAAACA AL590385 GU-CAGGAU-GGCCG-AGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCC---CU---GGAGG----CGUGGGUUCGAA-UCCCAC-UCCUG-ACA Seq gNgcaNg_UaGcuca_a_____cu__gg_______u_NAgagCg___ccNcccu_gaNaa_ggNggaggucgcggguUCgaa_ucccgN_ucNggcNCa AB013372 (((((((-..((((.-.-----..--..-------.-..)))).---(((((-(-....).))))).....(((((.....---)))))..))))))). AB013373 (((((((-..((((.-.------.--..-------.--.)))).---((((((.-....)-))))).....(((((......-.)))))--))))))). AE000930 -(((((.-..((((...-----..--..-------.--.)))).---(((((.....-.-.))))).....(((((......-.)))))-.-))))).. AB067577 ((((((.-..((((.-.-----..--..-------.-..)))).---(((((..-.....-))))).....(((((...-....)))))--.)))))). AF034440 (((.(((-..((((.-.-----..--.-----------.)))).---(((((.(-....)-)))))....-((((-......---))))--))).))). AL590385 ((-(((((.-((((.-.(((((.......))))).....))))...((((((.---..---)))))----)(((((......-.)))))-)))))-)). Str(50%) (((((((_..((((._._____..__.._______._..)))).___(((((.._....._))))).....(((((......_.)))))_.))))))). Str(60%) ((((((._..((((._._____..__.._______._..)))).___(((((.._....._))))).....(((((......_.)))))_..)))))). Str(70%) ((((((._..((((._._____..__.._______._..)))).___(((((.._....._))))).....(((((......_.)))))_..)))))). Str(80%) ((((((._..((((._._____..__.._______._..)))).___(((((.._....._))))).....(((((......_.)))))_..)))))). Str(90%) .(..((._..((((._._____..__.._______._..)))).___(((((.._....._))))).....((((......._..))))_..))..)..or you can use the following more easier format:
Name1 AUGCUUUGCAU Name2 AUGGGGGCCAU Name3 AAAAUUUUUUU Name1 ((((...)))) Name2 ((((...)))) Name3 ((((...))))Note: use CBCDetect only with RNA data NOT with DNA.
The output of CBCDetect is a count- (resp. a distance) matrix (uncorrected p-distances)of CBCs, which could be used as input for cbcTree.